head	1.1361;
access;
symbols
	release-2-12:1.1358
	release-2-12-beta-1:1.1357
	release-2-11:1.1349
	release-2-11-beta-2:1.1348
	release-2-11-beta-1:1.1347
	release-2-10:1.1341
	release-2-10-beta-2:1.1339
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	release-2-9:1.1320
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	release-2-8-beta-3:1.1299
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	release-2-7:1.1282
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	release-2-5:1.1205
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	release-2-0-beta-3:1.1068
	release-2-0-beta-2:1.1068
	release-alpha-1:1.1051
	development-4:1.1043
	development-3:1.1008
	development-2:1.1000
	development-1-1:1.778.0.2
	development-1:1.778
	development-0-1:1.777.0.2
	development-0:1.777;
locks; strict;
comment	@# @;


1.1361
date	2017.03.30.20.06.13;	author jim;	state Exp;
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1.1360
date	2017.03.22.22.06.33;	author jim;	state Exp;
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1.1359
date	2017.02.15.18.24.29;	author jim;	state Exp;
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1.1358
date	2016.12.21.15.42.24;	author jim;	state Exp;
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1.1357
date	2016.11.01.22.01.10;	author jim;	state Exp;
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1.1356
date	2016.10.07.16.14.01;	author jim;	state Exp;
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1.1355
date	2016.09.29.20.31.43;	author jim;	state Exp;
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1.1354
date	2016.09.27.15.40.31;	author jim;	state Exp;
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1.1353
date	2016.09.14.15.46.49;	author jim;	state Exp;
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1.1352
date	2016.03.18.15.05.09;	author jim;	state Exp;
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1.1351
date	2016.02.26.02.56.29;	author jim;	state Exp;
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1.1350
date	2016.02.10.15.26.16;	author jim;	state Exp;
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1.1349
date	2015.12.20.22.30.25;	author jim;	state Exp;
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1.1348
date	2015.12.03.21.48.42;	author jim;	state Exp;
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1.1347
date	2015.11.07.17.11.20;	author jim;	state Exp;
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1.1346
date	2015.10.09.20.47.16;	author jim;	state Exp;
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1.1345
date	2015.09.25.21.10.43;	author jim;	state Exp;
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1.1344
date	2015.09.22.21.29.06;	author jim;	state Exp;
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1.1343
date	2015.08.07.20.34.10;	author jim;	state Exp;
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1.1342
date	2015.03.13.20.20.02;	author jim;	state Exp;
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1.1341
date	2014.12.06.16.49.48;	author jim;	state Exp;
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1.1340
date	2014.11.23.21.25.32;	author jim;	state Exp;
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1.1339
date	2014.11.15.16.46.41;	author jim;	state Exp;
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1.1338
date	2014.10.30.20.38.07;	author jim;	state Exp;
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1.1337
date	2014.08.20.21.27.16;	author jim;	state Exp;
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1.1336
date	2014.05.09.21.39.03;	author jim;	state Exp;
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1.1335
date	2013.11.20.21.50.06;	author jim;	state Exp;
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1.1334
date	2013.07.10.17.18.24;	author jim;	state Exp;
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1.1333
date	2013.06.19.22.19.54;	author jim;	state Exp;
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1.1332
date	2013.06.12.20.00.31;	author jim;	state Exp;
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1.1331
date	2013.05.21.17.26.57;	author dhardy;	state Exp;
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1.1330
date	2013.04.26.18.54.49;	author jim;	state Exp;
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1.1329
date	2013.03.03.20.05.18;	author jim;	state Exp;
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1.1328
date	2013.01.18.15.10.47;	author jim;	state Exp;
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1.1327
date	2012.12.04.21.51.23;	author dhardy;	state Exp;
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1.1326
date	2012.09.20.16.44.29;	author jim;	state Exp;
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1.1325
date	2012.08.21.18.33.04;	author jim;	state Exp;
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1.1324
date	2012.08.10.19.12.37;	author bhatele;	state Exp;
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1.1323
date	2012.08.07.20.39.47;	author chaomei2;	state Exp;
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1.1322
date	2012.08.04.22.35.58;	author jim;	state Exp;
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1.1321
date	2012.05.22.20.50.42;	author dhardy;	state Exp;
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1.1320
date	2012.04.27.15.53.24;	author jim;	state Exp;
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1.1319
date	2012.04.05.22.09.46;	author jim;	state Exp;
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1.1318
date	2012.04.04.19.38.41;	author dhardy;	state Exp;
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1.1317
date	2012.03.26.19.51.40;	author jim;	state Exp;
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1.1316
date	2012.03.19.03.49.02;	author jim;	state Exp;
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1.1315
date	2012.03.15.20.12.08;	author jim;	state Exp;
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1.1314
date	2012.03.13.17.02.52;	author jim;	state Exp;
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1.1313
date	2012.03.08.22.55.47;	author jim;	state Exp;
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1.1312
date	2012.02.21.14.43.44;	author dtanner;	state Exp;
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1.1311
date	2012.02.17.02.13.06;	author jim;	state Exp;
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1.1310
date	2012.01.21.21.24.52;	author jim;	state Exp;
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1.1309
date	2012.01.14.21.55.45;	author jim;	state Exp;
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1.1308
date	2012.01.13.17.08.14;	author jim;	state Exp;
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1.1307
date	2011.12.13.00.11.35;	author jim;	state Exp;
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1.1306
date	2011.12.12.22.59.50;	author jim;	state Exp;
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1.1305
date	2011.12.06.21.37.52;	author dtanner;	state Exp;
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1.1304
date	2011.08.19.07.05.35;	author jim;	state Exp;
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1.1303
date	2011.08.16.21.24.59;	author dhardy;	state Exp;
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1.1302
date	2011.08.14.14.18.22;	author dhardy;	state Exp;
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1.1301
date	2011.08.14.13.38.43;	author dhardy;	state Exp;
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1.1300
date	2011.05.25.20.51.23;	author jim;	state Exp;
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1.1299
date	2011.05.19.16.19.59;	author jim;	state Exp;
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1.1298
date	2011.05.11.15.37.16;	author jim;	state Exp;
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1.1297
date	2011.05.10.18.10.58;	author jim;	state Exp;
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1.1296
date	2011.05.09.15.40.48;	author jim;	state Exp;
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1.1295
date	2011.05.08.19.29.33;	author jim;	state Exp;
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1.1294
date	2011.04.26.08.30.24;	author chaomei2;	state Exp;
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1.1293
date	2011.04.26.08.24.18;	author chaomei2;	state Exp;
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1.1292
date	2011.04.04.02.54.38;	author chaomei2;	state Exp;
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1.1291
date	2011.03.25.02.20.18;	author jim;	state Exp;
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1.1290
date	2011.03.18.19.01.03;	author jim;	state Exp;
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1.1289
date	2011.03.18.16.37.05;	author jim;	state Exp;
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1.1288
date	2011.03.18.07.22.45;	author chaomei2;	state Exp;
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1.1287
date	2011.03.09.14.31.18;	author jim;	state Exp;
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1.1286
date	2011.01.26.21.03.44;	author jim;	state Exp;
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1.1285
date	2010.12.15.23.19.41;	author ryanmcgreevy;	state Exp;
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1.1284
date	2010.11.30.18.33.27;	author dtanner;	state Exp;
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1.1283
date	2010.11.13.00.50.37;	author chaomei2;	state Exp;
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1.1282
date	2010.10.13.16.27.00;	author jim;	state Exp;
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1.1281
date	2010.09.17.14.40.00;	author jim;	state Exp;
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1.1280
date	2010.09.14.18.07.48;	author jim;	state Exp;
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1.1279
date	2010.09.14.17.48.47;	author jim;	state Exp;
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1.1278
date	2010.08.02.22.05.18;	author jim;	state Exp;
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1.1277
date	2010.08.02.20.38.25;	author jim;	state Exp;
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1.1276
date	2010.07.28.19.21.00;	author jim;	state Exp;
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1.1275
date	2010.07.02.21.17.00;	author jim;	state Exp;
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1.1274
date	2010.07.01.22.03.31;	author jim;	state Exp;
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1.1273
date	2010.07.01.18.57.31;	author jim;	state Exp;
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1.1272
date	2010.06.22.22.42.26;	author jim;	state Exp;
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1.1271
date	2010.04.23.22.02.12;	author sarood;	state Exp;
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1.1270
date	2010.02.15.17.50.23;	author jim;	state Exp;
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1.1269
date	2010.01.20.22.23.38;	author jim;	state Exp;
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1.1268
date	2010.01.19.22.11.57;	author dhardy;	state Exp;
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1.1267
date	2010.01.19.19.58.32;	author jim;	state Exp;
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1.1266
date	2010.01.17.22.34.20;	author jim;	state Exp;
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1.1265
date	2010.01.12.21.50.21;	author jim;	state Exp;
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1.1264
date	2010.01.12.21.35.05;	author jim;	state Exp;
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1.1263
date	2010.01.12.20.04.50;	author jim;	state Exp;
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1.1262
date	2009.12.02.23.12.34;	author emeneses;	state Exp;
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1.1261
date	2009.11.11.05.19.01;	author jim;	state Exp;
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1.1260
date	2009.11.11.05.01.47;	author jim;	state Exp;
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1.1259
date	2009.11.11.04.46.20;	author jim;	state Exp;
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1.1258
date	2009.11.11.04.18.34;	author jim;	state Exp;
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1.1257
date	2009.11.06.23.03.04;	author jim;	state Exp;
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1.1256
date	2009.10.27.18.52.28;	author brunner;	state Exp;
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1.1255
date	2009.08.12.22.53.46;	author char;	state Exp;
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1.1254
date	2009.07.20.20.55.03;	author brunner;	state Exp;
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1.1253
date	2009.05.19.05.11.08;	author jim;	state Exp;
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1.1252
date	2009.05.07.19.11.58;	author jim;	state Exp;
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1.1251
date	2009.03.13.20.30.00;	author jim;	state Exp;
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1.1250
date	2009.03.13.18.19.45;	author jim;	state Exp;
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1.1249
date	2009.03.12.21.54.20;	author jim;	state Exp;
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1.1248
date	2009.03.07.21.52.06;	author jim;	state Exp;
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1.1247
date	2009.02.13.15.12.54;	author bhatele;	state Exp;
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1.1246
date	2009.02.07.01.33.13;	author jim;	state Exp;
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1.1245
date	2009.02.06.23.13.09;	author jim;	state Exp;
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1.1244
date	2009.02.06.19.06.58;	author jim;	state Exp;
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1.1243
date	2008.12.19.20.40.23;	author jim;	state Exp;
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1.1242
date	2008.12.17.22.27.47;	author sameer;	state Exp;
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1.1241
date	2008.12.15.16.58.29;	author chaomei2;	state Exp;
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1.1240
date	2008.12.09.20.11.29;	author jim;	state Exp;
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1.1239
date	2008.11.12.23.18.50;	author jim;	state Exp;
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1.1238
date	2008.10.23.22.22.19;	author brunner;	state Exp;
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1.1237
date	2008.09.18.21.48.46;	author char;	state Exp;
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1.1236
date	2008.06.18.19.08.41;	author kunzman;	state Exp;
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1.1235
date	2008.06.17.21.21.22;	author chaomei2;	state Exp;
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1.1234
date	2008.05.28.21.23.13;	author jim;	state Exp;
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1.1233
date	2008.05.20.19.56.35;	author jim;	state Exp;
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1.1232
date	2008.04.08.16.23.40;	author jim;	state Exp;
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1.1231
date	2008.04.08.02.30.21;	author jim;	state Exp;
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1.1230
date	2008.03.07.00.59.34;	author chaomei2;	state Exp;
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1.1229
date	2007.11.07.21.36.12;	author bhatele;	state Exp;
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1.1228
date	2007.10.30.02.25.57;	author dbwells2;	state Exp;
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1.1227
date	2007.10.18.21.29.09;	author chaomei2;	state Exp;
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1.1226
date	2007.10.15.19.26.03;	author chaomei2;	state Exp;
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1.1225
date	2007.03.16.22.34.28;	author chaomei2;	state Exp;
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1.1224
date	2006.12.18.22.18.30;	author dbwells2;	state Exp;
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1.1223
date	2006.08.30.04.19.25;	author jim;	state Exp;
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1.1222
date	2006.08.16.19.24.18;	author jim;	state Exp;
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1.1221
date	2006.08.15.20.00.13;	author jim;	state Exp;
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1.1220
date	2006.08.15.00.37.38;	author jim;	state Exp;
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1.1219
date	2006.06.07.21.58.10;	author jim;	state Exp;
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1.1218
date	2006.06.07.21.22.31;	author jim;	state Exp;
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1.1217
date	2006.06.06.05.20.27;	author jim;	state Exp;
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1.1216
date	2006.06.05.23.31.12;	author jim;	state Exp;
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1.1215
date	2006.04.17.16.53.36;	author chaomei2;	state Exp;
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1.1214
date	2006.04.01.21.05.23;	author jim;	state Exp;
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1.1213
date	2005.08.01.15.52.58;	author jim;	state Exp;
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date	2005.07.22.18.50.58;	author jim;	state Exp;
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date	2005.07.21.16.23.05;	author jim;	state Exp;
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1.1210
date	2005.07.20.21.22.51;	author jim;	state Exp;
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date	2005.05.27.22.56.44;	author jim;	state Exp;
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date	2005.05.27.19.32.30;	author jim;	state Exp;
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date	2004.10.07.20.27.54;	author jim;	state Exp;
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date	2004.02.20.21.34.46;	author jim;	state Exp;
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date	2003.09.26.22.08.45;	author jim;	state Exp;
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date	2003.09.26.19.44.52;	author jim;	state Exp;
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date	2003.09.19.01.02.17;	author jim;	state Exp;
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date	2003.09.12.21.13.22;	author jim;	state Exp;
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1.1201
date	2003.08.25.23.17.34;	author jim;	state Exp;
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1.1200
date	2003.08.11.18.25.53;	author jim;	state Exp;
branches;
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1.1199
date	2003.08.04.20.17.38;	author jim;	state Exp;
branches;
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1.1198
date	2003.08.04.14.59.31;	author jim;	state Exp;
branches;
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1.1197
date	2003.07.26.20.54.06;	author sameer;	state Exp;
branches;
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1.1196
date	2003.07.02.16.14.31;	author jim;	state Exp;
branches;
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1.1195
date	2003.06.23.21.50.08;	author gzheng;	state Exp;
branches;
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1.1194
date	2003.06.16.23.56.07;	author jim;	state Exp;
branches;
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1.1193
date	2003.05.27.21.06.35;	author jim;	state Exp;
branches;
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1.1192
date	2003.04.09.22.51.12;	author barryi;	state Exp;
branches;
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1.1191
date	2003.04.07.06.20.50;	author justin;	state Exp;
branches;
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1.1190
date	2003.04.04.15.54.58;	author jim;	state Exp;
branches;
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1.1189
date	2003.01.29.02.37.33;	author jim;	state Exp;
branches;
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1.1188
date	2003.01.29.02.24.16;	author jim;	state Exp;
branches;
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1.1187
date	2002.09.20.15.11.58;	author jim;	state Exp;
branches;
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1.1186
date	2002.09.09.15.45.37;	author jim;	state Exp;
branches;
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1.1185
date	2002.08.27.18.45.39;	author jim;	state Exp;
branches;
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1.1184
date	2002.08.02.21.46.20;	author justin;	state Exp;
branches;
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1.1183
date	2002.06.13.21.52.00;	author jim;	state Exp;
branches;
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1.1182
date	2002.06.11.22.27.16;	author jim;	state Exp;
branches;
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1.1181
date	2002.06.04.16.16.23;	author jim;	state Exp;
branches;
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1.1180
date	2002.05.01.21.49.31;	author gzheng;	state Exp;
branches;
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1.1179
date	2002.04.27.01.07.46;	author justin;	state Exp;
branches;
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1.1178
date	2002.04.16.22.56.05;	author jim;	state Exp;
branches;
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1.1177
date	2002.03.08.22.46.34;	author jim;	state Exp;
branches;
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1.1176
date	2002.02.19.23.05.01;	author jim;	state Exp;
branches;
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1.1175
date	2002.02.19.22.48.38;	author jim;	state Exp;
branches;
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1.1174
date	2002.02.19.21.43.04;	author jim;	state Exp;
branches;
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1.1173
date	2002.02.19.19.32.49;	author jim;	state Exp;
branches;
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1.1172
date	2002.02.13.17.11.45;	author jim;	state Exp;
branches;
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1.1171
date	2002.02.13.16.35.08;	author jim;	state Exp;
branches;
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1.1170
date	2002.01.23.19.44.39;	author jim;	state Exp;
branches;
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1.1169
date	2002.01.10.18.58.08;	author jim;	state Exp;
branches;
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1.1168
date	2001.12.13.22.08.00;	author gzheng;	state Exp;
branches;
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1.1167
date	2001.12.13.18.44.24;	author gzheng;	state Exp;
branches;
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1.1166
date	2001.12.13.06.17.56;	author gzheng;	state Exp;
branches;
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1.1165
date	2001.11.09.22.58.16;	author pgrayson;	state Exp;
branches;
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1.1164
date	2001.11.01.18.40.24;	author jim;	state Exp;
branches;
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1.1163
date	2001.10.23.18.23.09;	author jim;	state Exp;
branches;
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1.1162
date	2001.10.11.18.34.57;	author gzheng;	state Exp;
branches;
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1.1161
date	2001.10.10.21.17.47;	author pgrayson;	state Exp;
branches;
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1.1160
date	2001.10.10.20.14.16;	author jim;	state Exp;
branches;
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1.1159
date	2001.09.06.19.15.16;	author gzheng;	state Exp;
branches;
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1.1158
date	2001.08.02.00.39.18;	author jim;	state Exp;
branches;
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1.1157
date	2001.08.02.00.25.10;	author jim;	state Exp;
branches;
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1.1156
date	2001.07.04.05.26.59;	author fzhu;	state Exp;
branches;
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1.1155
date	2001.06.13.16.11.31;	author fzhu;	state Exp;
branches;
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1.1154
date	2001.05.22.20.03.09;	author jim;	state Exp;
branches;
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1.1153
date	2001.05.03.19.57.24;	author jim;	state Exp;
branches;
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1.1152
date	2001.03.29.00.48.15;	author jim;	state Exp;
branches;
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1.1151
date	2001.03.22.17.42.02;	author justin;	state Exp;
branches;
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1.1150
date	2001.03.19.05.47.25;	author gzheng;	state Exp;
branches;
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1.1149
date	2001.03.03.18.10.33;	author gzheng;	state Exp;
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1.1148
date	2001.03.01.17.15.51;	author jim;	state Exp;
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1.1147
date	2001.02.23.02.03.21;	author jim;	state Exp;
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1.1146
date	2001.02.20.23.42.49;	author jim;	state Exp;
branches;
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1.1145
date	2001.02.20.20.14.38;	author jim;	state Exp;
branches;
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1.1144
date	2001.02.19.17.22.35;	author jim;	state Exp;
branches;
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1.1143
date	2001.02.16.22.36.39;	author jim;	state Exp;
branches;
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1.1142
date	2001.02.16.22.06.33;	author jim;	state Exp;
branches;
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1.1141
date	2001.02.15.21.27.20;	author jim;	state Exp;
branches;
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1.1140
date	2001.02.12.16.38.55;	author jim;	state Exp;
branches;
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1.1139
date	2001.02.12.16.19.01;	author jim;	state Exp;
branches;
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1.1138
date	2001.01.31.21.32.24;	author jim;	state Exp;
branches;
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1.1137
date	2001.01.20.21.33.15;	author jim;	state Exp;
branches;
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1.1136
date	2000.10.04.01.18.00;	author jim;	state Exp;
branches;
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1.1135
date	2000.09.29.19.45.13;	author jim;	state Exp;
branches;
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1.1134
date	2000.09.25.16.43.21;	author jim;	state Exp;
branches;
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1.1133
date	2000.09.22.22.10.58;	author jim;	state Exp;
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1.1132
date	2000.09.22.21.48.21;	author jim;	state Exp;
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1.1131
date	2000.09.18.19.41.17;	author jim;	state Exp;
branches;
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1.1130
date	2000.09.18.16.43.11;	author jim;	state Exp;
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1.1129
date	2000.09.18.16.25.48;	author jim;	state Exp;
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1.1128
date	2000.09.15.20.43.07;	author jim;	state Exp;
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1.1127
date	2000.09.14.22.45.02;	author jim;	state Exp;
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1.1126
date	2000.09.14.22.13.26;	author jim;	state Exp;
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1.1125
date	2000.09.14.20.01.00;	author jim;	state Exp;
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1.1124
date	2000.09.14.17.46.08;	author jim;	state Exp;
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1.1123
date	2000.09.01.22.51.23;	author jim;	state Exp;
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1.1122
date	2000.08.31.22.03.43;	author jim;	state Exp;
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1.1121
date	2000.08.29.22.10.31;	author jim;	state Exp;
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1.1120
date	2000.08.29.02.54.52;	author jim;	state Exp;
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1.1119
date	2000.08.28.20.04.57;	author jim;	state Exp;
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1.1118
date	2000.08.28.19.45.04;	author jim;	state Exp;
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1.1117
date	2000.07.19.22.46.01;	author jim;	state Exp;
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1.1116
date	2000.07.19.22.16.19;	author jim;	state Exp;
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1.1115
date	2000.06.29.04.54.56;	author jim;	state Exp;
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1.1114
date	2000.04.27.16.33.00;	author jim;	state Exp;
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1.1113
date	2000.03.24.16.48.05;	author jim;	state Exp;
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1.1112
date	2000.03.16.17.06.58;	author jim;	state Exp;
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1.1111
date	2000.03.16.16.19.27;	author jim;	state Exp;
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1.1110
date	2000.03.13.16.47.16;	author jim;	state Exp;
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1.1109
date	2000.03.12.21.33.31;	author brunner;	state Exp;
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1.1108
date	2000.03.07.00.19.45;	author jim;	state Exp;
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1.1107
date	2000.02.10.00.21.15;	author jim;	state Exp;
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1.1106
date	2000.01.19.22.19.42;	author jim;	state Exp;
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1.1105
date	99.12.21.22.16.38;	author jim;	state Exp;
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1.1104
date	99.12.15.23.50.48;	author jim;	state Exp;
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1.1103
date	99.12.15.23.30.59;	author jim;	state Exp;
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1.1102
date	99.12.15.16.51.04;	author jim;	state Exp;
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1.1101
date	99.12.06.22.17.51;	author jim;	state Exp;
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1.1100
date	99.12.05.22.19.47;	author jim;	state Exp;
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1.1099
date	99.12.04.22.43.29;	author brunner;	state Exp;
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1.1098
date	99.12.03.20.48.07;	author jim;	state Exp;
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1.1097
date	99.12.03.17.34.42;	author justin;	state Exp;
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1.1096
date	99.11.11.16.16.34;	author jim;	state Exp;
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1.1095
date	99.11.10.15.37.18;	author jim;	state Exp;
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1.1094
date	99.11.03.21.05.58;	author jim;	state Exp;
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1.1093
date	99.10.30.20.30.31;	author jim;	state Exp;
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1.1092
date	99.10.29.22.35.09;	author jim;	state Exp;
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1.1091
date	99.10.29.22.18.13;	author jim;	state Exp;
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1.1090
date	99.10.25.21.35.53;	author jim;	state Exp;
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1.1089
date	99.10.08.16.35.55;	author jim;	state Exp;
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1.1088
date	99.10.08.15.42.14;	author jim;	state Exp;
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1.1087
date	99.09.24.20.19.55;	author jim;	state Exp;
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1.1086
date	99.09.15.18.08.05;	author brunner;	state Exp;
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1.1085
date	99.09.09.21.33.00;	author jim;	state Exp;
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1.1084
date	99.09.08.23.02.13;	author jim;	state Exp;
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1.1083
date	99.09.08.16.05.38;	author jim;	state Exp;
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1.1082
date	99.09.02.23.04.18;	author justin;	state Exp;
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1.1081
date	99.08.25.22.14.25;	author brunner;	state Exp;
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1.1080
date	99.08.16.22.18.52;	author jim;	state Exp;
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1.1079
date	99.08.16.21.23.36;	author brunner;	state Exp;
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1.1078
date	99.07.02.22.07.35;	author jim;	state Exp;
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1.1077
date	99.07.01.20.58.27;	author jim;	state Exp;
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1.1076
date	99.06.08.14.51.34;	author jim;	state Exp;
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1.1075
date	99.06.03.16.50.51;	author jim;	state Exp;
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1.1074
date	99.05.26.22.25.14;	author jim;	state Exp;
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1.1073
date	99.05.25.21.50.37;	author jim;	state Exp;
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1.1072
date	99.05.11.23.55.59;	author brunner;	state Exp;
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1.1071
date	99.05.07.19.19.08;	author jim;	state Exp;
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1.1070
date	99.04.29.15.29.32;	author jim;	state Exp;
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1.1069
date	99.03.18.22.05.53;	author jim;	state Exp;
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1.1068
date	98.08.21.02.13.39;	author jim;	state Exp;
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1.1067
date	98.08.21.01.17.31;	author jim;	state Exp;
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1.1066
date	98.05.21.22.37.08;	author hurwitz;	state Exp;
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1.1065
date	98.04.30.04.52.57;	author jim;	state Exp;
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1.1064
date	98.04.15.22.12.35;	author jim;	state Exp;
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1.1063
date	98.04.14.03.18.37;	author jim;	state Exp;
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1.1062
date	98.04.10.04.14.59;	author jim;	state Exp;
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1.1061
date	98.04.06.16.33.05;	author jim;	state Exp;
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1.1060
date	98.03.31.04.56.47;	author jim;	state Exp;
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1.1059
date	98.02.10.06.44.49;	author jim;	state Exp;
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1.1058
date	98.02.10.05.33.35;	author jim;	state Exp;
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1.1057
date	98.02.09.16.24.29;	author brunner;	state Exp;
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1.1056
date	98.01.06.05.36.44;	author jim;	state Exp;
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1.1055
date	98.01.05.20.38.14;	author sergei;	state Exp;
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1.1054
date	97.12.26.23.10.23;	author milind;	state Exp;
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1.1053
date	97.12.19.23.50.41;	author jim;	state Exp;
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1.1052
date	97.11.07.20.17.06;	author milind;	state Exp;
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1.1051
date	97.10.01.16.45.52;	author milind;	state Exp;
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1.1050
date	97.09.30.21.40.57;	author brunner;	state Exp;
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1.1049
date	97.09.28.10.23.40;	author milind;	state Exp;
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1.1048
date	97.09.12.23.04.26;	author jim;	state Exp;
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1.1047
date	97.08.12.22.18.36;	author milind;	state Exp;
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1.1046
date	97.08.12.16.37.50;	author milind;	state Exp;
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1.1045
date	97.07.09.21.26.36;	author milind;	state Exp;
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1.1044
date	97.07.08.15.48.04;	author milind;	state Exp;
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1.1043
date	97.04.22.04.17.45;	author jim;	state Exp;
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1.1042
date	97.04.08.17.11.47;	author nealk;	state Exp;
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1.1041
date	97.04.07.21.09.42;	author brunner;	state Exp;
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1.1040
date	97.04.07.00.05.02;	author brunner;	state Exp;
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1.1039
date	97.04.06.22.46.02;	author ari;	state Exp;
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1.1038
date	97.04.05.04.54.01;	author brunner;	state Exp;
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1.1037
date	97.04.04.23.34.07;	author milind;	state Exp;
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1.1036
date	97.04.04.20.17.48;	author nealk;	state Exp;
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1.1035
date	97.04.03.19.29.29;	author nealk;	state Exp;
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1.1034
date	97.04.02.17.07.27;	author nealk;	state Exp;
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1.1033
date	97.03.27.21.30.56;	author jim;	state Exp;
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1.1032
date	97.03.27.20.25.07;	author brunner;	state Exp;
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1.1031
date	97.03.20.23.51.42;	author ari;	state Exp;
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1.1030
date	97.03.19.11.52.26;	author ari;	state Exp;
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1.1029
date	97.03.19.05.49.06;	author jim;	state Exp;
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1.1028
date	97.03.17.15.50.19;	author nealk;	state Exp;
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1.1027
date	97.03.17.02.52.00;	author jim;	state Exp;
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1.1026
date	97.03.15.22.14.20;	author jim;	state Exp;
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1.1025
date	97.03.14.21.38.56;	author ari;	state Exp;
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1.1024
date	97.03.11.05.33.07;	author jim;	state Exp;
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1.1023
date	97.03.10.17.59.37;	author ari;	state Exp;
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1.1022
date	97.03.10.17.39.38;	author ari;	state Exp;
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1.1021
date	97.03.06.22.05.29;	author ari;	state Exp;
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1.1020
date	97.03.04.22.35.49;	author ari;	state Exp;
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desc
@@


1.1361
log
@From Antti-Pekka Hynninen, offload bonded terms to GPU (bondedCUDA 0 to disable) and support non-orthorhombic periodic cell with new non-bonded and PME kernels.
@
text
@# pass version/platform information to compile
NAMD_VERSION = 2.12

# compiler flags (Win32 overrides)
COPTI = -I
COPTC = -c
COPTD = -D
COPTO = -o $(SPACE)

# Unix commands

ECHO = echo
MOVE = mv
MKDIR = mkdir -p
COPY = cp
RM = rm -f
LDD = ldd

# pass version/platform information to compile
RELEASE=$(COPTD)NAMD_VERSION=\"$(NAMD_VERSION)\" $(COPTD)NAMD_PLATFORM=\"$(NAMD_PLATFORM)\" $(RELEASEFLAGS)

# directories
SRCDIR = src
DSTDIR = obj
INCDIR = inc
DPMTADIR=dpmta-2.6
DPMEDIR=dpme2
PLUGINSRCDIR= plugins/molfile_plugin/src
PLUGININCDIR= plugins/include
SBSRCDIR = sb/src

MKDSTDIR = $(DSTDIR)/.exists
MKINCDIR = $(INCDIR)/.exists

# comment/uncomment these lines for (D)PMTA routines
#DPMTAINCL=$(COPTI)$(DPMTADIR)/mpole $(COPTI)$(DPMTADIR)/src
#DPMTALIB=-L$(DPMTADIR)/mpole -L$(DPMTADIR)/src -ldpmta2 -lmpole -lpvmc
#DPMTAFLAGS=$(COPTD)DPMTA
#DPMTA=$(DPMTAINCL) $(DPMTAFLAGS)
#DPMTALIBS=$(DPMTADIR)/mpole/libmpole.a $(DPMTADIR)/src/libdpmta2.a

# comment/uncomment these lines for DPME routines
#DPMEINCL=$(COPTI)$(DPMEDIR)
#DPMELIB=-L$(DPMEDIR) -ldpme
#DPMEFLAGS=$(COPTD)DPME
#DPME=$(DPMEINCL) $(DPMEFLAGS)
#DPMELIBS= $(DPMEDIR)/libdpme.a

# comment/uncomment these lines for FMM routines
#
# ufmmlap library from J. Huang - http://fastmultipole.org/Main/FMMSuite/
#   (ufmmlap = Uniform FMM Laplace Solver)
#
# Options below assume building with Gnu compilers.
# Define FMMDIR in Make.config file.
#
#FMMNAME=ufmmlap
#FMMINCL=$(COPTI)$(FMMDIR)/src
#FMMLIB=-L$(FMMDIR)/src -l$(FMMNAME) -lgfortran
#FMMFLAGS=$(COPTD)FMM_SOLVER
#FMM=$(FMMINCL) $(FMMFLAGS)
#FMMLIBS=$(FMMDIR)/src/lib$(FMMNAME).a

# to compile a memory optimized version, uncomment or config --with-memopt
#MEMOPT=-DMEM_OPT_VERSION
# to compile version that uses node-aware proxy send/recv spanning tree,
# add -DNODEAWARE_PROXY_SPANNINGTREE to the variable EXTRADEFINES
#EXTRADEFINES=-DREMOVE_PROXYDATAMSG_EXTRACOPY -DREMOVE_PROXYRESULTMSG_EXTRACOPY
EXTRADEFINES=-DREMOVE_PROXYRESULTMSG_EXTRACOPY -DNODEAWARE_PROXY_SPANNINGTREE -DUSE_NODEPATCHMGR -DBONDED_CUDA -DUSE_HOMETUPLES
EXTRAINCS=
EXTRALINKLIBS=
# to compile namd using PAPI counters to measure flops and modify include and library path
# correspondingly
#EXTRADEFINES=-DREMOVE_PROXYRESULTMSG_EXTRACOPY -DMEASURE_NAMD_WITH_PAPI
#EXTRAINCS=-I$(HOME)/papi/include
#EXTRALINKLIBS=-lpapi -L$(HOME)/papi/lib

#If using the CkLoop library from Charm++ for PME calculation, first define macro
# USE_CKLOOP=1 for compiling the code, and then add "-module CkLoop" for linking.
CKLOOP = -DUSE_CKLOOP=1
CKLOOP_MODULE = -module CkLoop

# defaults for special cases
CXXTHREADOPTS = $(CXXOPTS) 
CXXSIMPARAMOPTS = $(CXXOPTS) 
CXXNOALIASOPTS = $(CXXOPTS) 
CXXCOLVAROPTS = $(CXXOPTS) 
CXXMEMUSAGE = $(CXX)
CUDACC = $(CXX)
CUDAOBJS =
NATIVEPATH = echo

include Make.config

# define below Make.config so Win32 can change default target to winall
default: all

# Add new source files here.

OBJS = \
	$(DSTDIR)/ComputeMoa.o \
	$(DSTDIR)/ComputeMsm.o \
	$(DSTDIR)/ComputeMsmMsa.o \
	$(DSTDIR)/ComputeMsmSerial.o \
        $(DSTDIR)/ComputeFmmSerial.o \
	$(DSTDIR)/msm.o \
	$(DSTDIR)/msm_longrng.o \
	$(DSTDIR)/msm_longrng_sprec.o \
	$(DSTDIR)/msm_setup.o \
	$(DSTDIR)/msm_shortrng.o \
	$(DSTDIR)/msm_shortrng_sprec.o \
	$(DSTDIR)/wkfutils.o \
	$(DSTDIR)/common.o \
	$(DSTDIR)/dcdlib.o \
	$(DSTDIR)/eabf1D.o \
	$(DSTDIR)/eabf2D.o \
	$(DSTDIR)/eabffunc.o \
	$(DSTDIR)/eabfTcl.o \
	$(DSTDIR)/erf.o \
	$(DSTDIR)/fitrms.o \
	$(DSTDIR)/main.o \
	$(DSTDIR)/mainfunc.o \
	$(DSTDIR)/memusage.o \
	$(DSTDIR)/strlib.o \
	$(DSTDIR)/AlgSeven.o \
	$(DSTDIR)/AlgRecBisection.o \
	$(DSTDIR)/AlgNbor.o \
	$(DSTDIR)/AtomMap.o \
	$(DSTDIR)/BackEnd.o \
	$(DSTDIR)/BroadcastMgr.o \
	$(DSTDIR)/BroadcastClient.o \
	$(DSTDIR)/CollectionMaster.o \
	$(DSTDIR)/CollectionMgr.o \
	$(DSTDIR)/Communicate.o \
	$(DSTDIR)/Compute.o \
	$(DSTDIR)/ComputeAngles.o \
	$(DSTDIR)/ComputeAniso.o \
	$(DSTDIR)/ComputeBonds.o \
	$(DSTDIR)/ComputeBondedCUDA.o \
	$(DSTDIR)/ComputeConsForce.o \
	$(DSTDIR)/ComputeConsForceMsgs.o \
	$(DSTDIR)/ComputeCrossterms.o \
	$(DSTDIR)/ComputeCUDAMgr.o \
	$(DSTDIR)/ComputeCylindricalBC.o \
	$(DSTDIR)/ComputeDihedrals.o \
	$(DSTDIR)/ComputeDPME.o \
	$(DSTDIR)/ComputeDPMEMsgs.o \
	$(DSTDIR)/ComputeDPMTA.o \
	$(DSTDIR)/ComputeEField.o \
	$(DSTDIR)/ComputeEwald.o \
	$(DSTDIR)/ComputeExt.o \
	$(DSTDIR)/ComputeQM.o \
	$(DSTDIR)/ComputeGBISser.o \
	$(DSTDIR)/ComputeGBIS.o \
	$(DSTDIR)/ComputeGromacsPair.o \
	$(DSTDIR)/ComputeLCPO.o \
	$(DSTDIR)/ComputeFullDirect.o \
	$(DSTDIR)/ComputeHomePatch.o \
	$(DSTDIR)/ComputeHomePatches.o \
	$(DSTDIR)/ComputeImpropers.o \
	$(DSTDIR)/ComputeGlobal.o \
	$(DSTDIR)/ComputeGlobalMsgs.o \
	$(DSTDIR)/ComputeGridForce.o \
	$(DSTDIR)/ComputeMap.o \
	$(DSTDIR)/ComputeMgr.o \
	$(DSTDIR)/ComputeNonbondedSelf.o \
	$(DSTDIR)/ComputeNonbondedPair.o \
	$(DSTDIR)/ComputeNonbondedUtil.o \
	$(DSTDIR)/ComputeNonbondedStd.o \
	$(DSTDIR)/ComputeNonbondedFEP.o \
	$(DSTDIR)/ComputeNonbondedGo.o \
	$(DSTDIR)/ComputeNonbondedTI.o \
	$(DSTDIR)/ComputeNonbondedLES.o \
	$(DSTDIR)/ComputeNonbondedPProf.o \
	$(DSTDIR)/ComputeNonbondedTabEnergies.o \
	$(DSTDIR)/ComputeNonbondedCUDA.o \
	$(DSTDIR)/ComputeNonbondedCUDAExcl.o \
	$(DSTDIR)/ComputeNonbondedMIC.o \
	$(DSTDIR)/ComputeNonbondedMICKernel.o \
	$(DSTDIR)/ComputePatch.o \
	$(DSTDIR)/ComputePatchPair.o \
	$(DSTDIR)/ComputePme.o \
	$(DSTDIR)/ComputePmeCUDA.o \
	$(DSTDIR)/ComputePmeCUDAMgr.o \
	$(DSTDIR)/OptPme.o \
	$(DSTDIR)/OptPmeRealSpace.o \
	$(DSTDIR)/ComputeRestraints.o \
	$(DSTDIR)/ComputeSphericalBC.o \
	$(DSTDIR)/ComputeStir.o \
	$(DSTDIR)/ComputeTclBC.o \
	$(DSTDIR)/ComputeThole.o \
	$(DSTDIR)/ConfigList.o \
	$(DSTDIR)/Controller.o \
	$(DSTDIR)/CudaComputeNonbonded.o \
	$(DSTDIR)/CudaNonbondedTables.o \
	$(DSTDIR)/CudaPmeSolver.o \
	$(DSTDIR)/CudaPmeSolverUtil.o \
	$(DSTDIR)/CudaUtils.o \
	$(DSTDIR)/ccsinterface.o \
	$(DSTDIR)/DataStream.o \
	$(DSTDIR)/DeviceCUDA.o \
	$(DSTDIR)/DumpBench.o \
        $(DSTDIR)/FreeEnergyAssert.o \
        $(DSTDIR)/FreeEnergyGroup.o \
        $(DSTDIR)/FreeEnergyLambda.o \
        $(DSTDIR)/FreeEnergyLambdMgr.o \
        $(DSTDIR)/FreeEnergyParse.o \
        $(DSTDIR)/FreeEnergyRestrain.o \
        $(DSTDIR)/FreeEnergyRMgr.o \
        $(DSTDIR)/FreeEnergyVector.o \
	$(DSTDIR)/fstream_namd.o \
	$(DSTDIR)/GlobalMaster.o \
	$(DSTDIR)/GlobalMasterServer.o \
	$(DSTDIR)/GlobalMasterTest.o \
	$(DSTDIR)/GlobalMasterIMD.o \
	$(DSTDIR)/GlobalMasterTcl.o \
	$(DSTDIR)/GlobalMasterSMD.o \
	$(DSTDIR)/GlobalMasterTMD.o \
  $(DSTDIR)/Matrix4Symmetry.o \
  $(DSTDIR)/GlobalMasterSymmetry.o \
	$(DSTDIR)/GlobalMasterFreeEnergy.o \
	$(DSTDIR)/GlobalMasterEasy.o \
	$(DSTDIR)/GlobalMasterMisc.o \
	$(DSTDIR)/colvar.o \
	$(DSTDIR)/colvaratoms.o \
	$(DSTDIR)/colvarbias.o \
	$(DSTDIR)/colvarbias_abf.o \
	$(DSTDIR)/colvarbias_alb.o \
	$(DSTDIR)/colvarbias_histogram.o \
	$(DSTDIR)/colvarbias_meta.o \
	$(DSTDIR)/colvarbias_restraint.o \
	$(DSTDIR)/colvarcomp.o \
	$(DSTDIR)/colvarcomp_angles.o \
	$(DSTDIR)/colvarcomp_coordnums.o \
	$(DSTDIR)/colvarcomp_distances.o \
	$(DSTDIR)/colvarcomp_protein.o \
	$(DSTDIR)/colvarcomp_rotations.o \
	$(DSTDIR)/colvardeps.o \
	$(DSTDIR)/colvargrid.o \
	$(DSTDIR)/colvarmodule.o \
	$(DSTDIR)/colvarparse.o \
	$(DSTDIR)/colvarproxy_namd.o \
	$(DSTDIR)/colvarscript.o \
	$(DSTDIR)/colvartypes.o \
	$(DSTDIR)/colvarvalue.o \
	$(DSTDIR)/GridForceGrid.o \
        $(DSTDIR)/GromacsTopFile.o \
	$(DSTDIR)/heap.o \
	$(DSTDIR)/HomePatch.o \
	$(DSTDIR)/IMDOutput.o \
	$(DSTDIR)/InfoStream.o \
	$(DSTDIR)/LdbCoordinator.o \
	$(DSTDIR)/LJTable.o \
	$(DSTDIR)/Measure.o \
	$(DSTDIR)/MGridforceParams.o \
	$(DSTDIR)/MStream.o \
	$(DSTDIR)/MigrateAtomsMsg.o \
	$(DSTDIR)/Molecule.o \
	$(DSTDIR)/Molecule2.o \
	$(DSTDIR)/GoMolecule.o \
        $(DSTDIR)/MoleculeQM.o \
	$(DSTDIR)/NamdCentLB.o \
	$(DSTDIR)/NamdNborLB.o \
	$(DSTDIR)/NamdHybridLB.o \
	$(DSTDIR)/NamdDummyLB.o \
	$(DSTDIR)/NamdState.o \
	$(DSTDIR)/NamdOneTools.o \
	$(DSTDIR)/Node.o \
	$(DSTDIR)/Output.o \
	$(DSTDIR)/Parameters.o \
	$(DSTDIR)/ParseOptions.o \
	$(DSTDIR)/Patch.o \
	$(DSTDIR)/PatchMgr.o \
	$(DSTDIR)/PatchMap.o \
	$(DSTDIR)/PDB.o \
	$(DSTDIR)/PDBData.o \
	$(DSTDIR)/PmeKSpace.o \
	$(DSTDIR)/PmeRealSpace.o \
	$(DSTDIR)/PmeSolver.o \
	$(DSTDIR)/ProcessorPrivate.o \
	$(DSTDIR)/ProxyMgr.o \
	$(DSTDIR)/ProxyPatch.o \
	$(DSTDIR)/Rebalancer.o \
	$(DSTDIR)/RecBisection.o \
	$(DSTDIR)/ReductionMgr.o \
	$(DSTDIR)/RefineOnly.o \
	$(DSTDIR)/RefineTorusLB.o \
	$(DSTDIR)/ScriptTcl.o \
	$(DSTDIR)/Sequencer.o \
	$(DSTDIR)/Set.o \
	$(DSTDIR)/Settle.o \
	$(DSTDIR)/SimParameters.o \
	$(DSTDIR)/SortAtoms.o \
	$(DSTDIR)/Sync.o \
	$(DSTDIR)/TclCommands.o \
	$(DSTDIR)/TorusLB.o \
	$(DSTDIR)/WorkDistrib.o \
	$(DSTDIR)/pub3dfft.o \
	$(DSTDIR)/vmdsock.o \
	$(DSTDIR)/parm.o \
	$(DSTDIR)/imd.o \
	$(DSTDIR)/CompressPsf.o \
	$(DSTDIR)/PluginIOMgr.o \
	$(DSTDIR)/DataExchanger.o \
	$(DSTDIR)/ParallelIOMgr.o 


# Add new modules here.

CIFILES = 	\
		$(INCDIR)/ComputeMoaMgr.decl.h \
		$(INCDIR)/ComputeMoaMgr.def.h \
		$(INCDIR)/ComputeMsmMgr.decl.h \
		$(INCDIR)/ComputeMsmMgr.def.h \
		$(INCDIR)/ComputeMsmMsaMgr.decl.h \
		$(INCDIR)/ComputeMsmMsaMgr.def.h \
		$(INCDIR)/ComputeMsmSerialMgr.decl.h \
		$(INCDIR)/ComputeMsmSerialMgr.def.h \
		$(INCDIR)/ComputeFmmSerialMgr.decl.h \
		$(INCDIR)/ComputeFmmSerialMgr.def.h \
		$(INCDIR)/BroadcastMgr.decl.h \
		$(INCDIR)/BroadcastMgr.def.h \
		$(INCDIR)/CollectionMaster.decl.h \
		$(INCDIR)/CollectionMaster.def.h \
		$(INCDIR)/CollectionMgr.decl.h \
		$(INCDIR)/CollectionMgr.def.h \
		$(INCDIR)/ComputeCUDAMgr.decl.h \
		$(INCDIR)/ComputeCUDAMgr.def.h \
		$(INCDIR)/ComputeMgr.decl.h \
		$(INCDIR)/ComputeMgr.def.h \
		$(INCDIR)/ComputeGridForceMgr.decl.h \
		$(INCDIR)/ComputeGridForceMgr.def.h \
		$(INCDIR)/ComputePmeMgr.decl.h \
		$(INCDIR)/ComputePmeMgr.def.h \
		$(INCDIR)/ComputePmeCUDAMgr.decl.h \
		$(INCDIR)/ComputePmeCUDAMgr.def.h \
		$(INCDIR)/CudaPmeSolver.decl.h \
		$(INCDIR)/CudaPmeSolver.def.h \
		$(INCDIR)/OptPmeMgr.decl.h \
		$(INCDIR)/OptPmeMgr.def.h \
		$(INCDIR)/PmeFFTLib.decl.h \
		$(INCDIR)/PmeFFTLib.def.h \
		$(INCDIR)/PmeSolver.decl.h \
		$(INCDIR)/PmeSolver.def.h \
		$(INCDIR)/ComputeExtMgr.decl.h \
		$(INCDIR)/ComputeExtMgr.def.h \
		$(INCDIR)/ComputeQMMgr.decl.h \
		$(INCDIR)/ComputeQMMgr.def.h \
		$(INCDIR)/ComputeGBISserMgr.decl.h \
		$(INCDIR)/ComputeGBISserMgr.def.h \
		$(INCDIR)/LdbCoordinator.decl.h \
		$(INCDIR)/LdbCoordinator.def.h \
		$(INCDIR)/NamdCentLB.decl.h \
		$(INCDIR)/NamdCentLB.def.h \
		$(INCDIR)/NamdNborLB.decl.h \
		$(INCDIR)/NamdNborLB.def.h \
		$(INCDIR)/NamdHybridLB.decl.h \
		$(INCDIR)/NamdHybridLB.def.h \
		$(INCDIR)/NamdDummyLB.decl.h \
		$(INCDIR)/NamdDummyLB.def.h \
		$(INCDIR)/Node.decl.h \
		$(INCDIR)/Node.def.h \
		$(INCDIR)/PatchMgr.decl.h \
		$(INCDIR)/PatchMgr.def.h \
		$(INCDIR)/ProxyMgr.decl.h \
		$(INCDIR)/ProxyMgr.def.h \
		$(INCDIR)/ReductionMgr.decl.h \
		$(INCDIR)/ReductionMgr.def.h \
		$(INCDIR)/Sync.decl.h \
		$(INCDIR)/Sync.def.h \
		$(INCDIR)/WorkDistrib.decl.h \
		$(INCDIR)/WorkDistrib.def.h \
		$(INCDIR)/ParallelIOMgr.decl.h \
		$(INCDIR)/ParallelIOMgr.def.h \
		$(INCDIR)/DataExchanger.decl.h \
		$(INCDIR)/DataExchanger.def.h \
		$(INCDIR)/main.decl.h \
		$(INCDIR)/main.def.h 

# Add new source files here.

PLUGINOBJS = \
	$(DSTDIR)/dcdplugin.o \
	$(DSTDIR)/jsplugin.o \
	$(DSTDIR)/namdbinplugin.o \
	$(DSTDIR)/pdbplugin.o \
	$(DSTDIR)/psfplugin.o

PLUGINLIB = $(PLUGINOBJS)

CUDAOBJSRAW = \
	$(DSTDIR)/ComputeBondedCUDAKernel.o \
	$(DSTDIR)/ComputeNonbondedCUDAKernel.o \
	$(DSTDIR)/ComputePmeCUDAKernel.o \
	$(DSTDIR)/CudaComputeGBISKernel.o \
	$(DSTDIR)/CudaComputeNonbondedKernel.o \
	$(DSTDIR)/CudaPmeSolverUtilKernel.o \
	$(DSTDIR)/CudaTileListKernel.o

CUDAOBJSRAWSTATIC = $(CUDAOBJSRAW) \
	$(DSTDIR)/CudaPmeSolverUtilKernel_dlink.o

$(DSTDIR)/CudaPmeSolverUtilKernel_dlink.o: $(DSTDIR)/CudaPmeSolverUtilKernel.o
	$(CUDACC) $(CUDADLINKOPTS) -v -lcufft_static -dlink $(DSTDIR)/CudaPmeSolverUtilKernel.o $(COPTO)$@@

SBOBJS = $(DSTDIR)/tcl_main.o $(SBLIB)

SBLIB = \
	$(DSTDIR)/tcl_psfgen.o \
	$(DSTDIR)/charmm_file.o \
	$(DSTDIR)/charmm_parse_topo_defs.o \
	$(DSTDIR)/extract_alias.o \
	$(DSTDIR)/hash.o \
	$(DSTDIR)/hasharray.o \
	$(DSTDIR)/memarena.o \
	$(DSTDIR)/pdb_file.o \
	$(DSTDIR)/pdb_file_extract.o \
	$(DSTDIR)/psf_file.o \
	$(DSTDIR)/psf_file_extract.o \
	$(DSTDIR)/topo_defs.o \
	$(DSTDIR)/topo_mol.o \
	$(DSTDIR)/topo_mol_output.o \
	$(DSTDIR)/topo_mol_pluginio.o \
	$(DSTDIR)/stringhash.o

# definitions for Charm routines
CHARMC = $(CHARM)/bin/charmc
CHARMXI = $(CHARM)/bin/charmc
CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1
CHARMLIB = $(CHARM)/lib
CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -module CkMulticast $(CKLOOP_MODULE)
#CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
#CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
#MSA = -DCHARM_HAS_MSA

# Libraries we may have changed
LIBS = $(CUDAOBJS) $(PLUGINLIB) $(SBLIB) $(DPMTALIBS) $(DPMELIBS) $(FMMLIBS) $(TCLDLL)

# CXX is platform dependent
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(FMM) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(PYTHON) $(FFT) $(CUDA) $(MIC) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS) $(MSA) $(CKLOOP)
CXXFLAGS = $(CXXBASEFLAGS) $(CXXOPTS)
CXXMICFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) $(CXXMICOPTS)
CXXTHREADFLAGS = $(CXXBASEFLAGS) $(CXXTHREADOPTS)
CXXSIMPARAMFLAGS = $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS)
CXXNOALIASFLAGS = $(CXXBASEFLAGS) $(CXXNOALIASOPTS)
CXXCOLVARFLAGS = $(CXXBASEFLAGS) $(CXXCOLVAROPTS)
GXXFLAGS = $(CXXBASEFLAGS) -DNO_STRSTREAM_H
CFLAGS = $(COPTI)$(SRCDIR) $(TCL) $(COPTS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
PLUGINGCCFLAGS = $(COPTI)$(PLUGINSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN
PLUGINCFLAGS = $(PLUGINGCCFLAGS) $(COPTS)
SBCFLAGS = $(COPTI)$(SBSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN -DPSFGEN_USEPLUGINS $(TCL) $(COPTS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
SBGCCFLAGS = $(COPTI)$(SBSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN -DPSFGEN_USEPLUGINS $(TCL) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)

# .ci preprocessing flags
CIPPFLAGS = $(CUDAFLAGS) -DBONDED_CUDA

# Add new executables here.

BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb charmrun

# This should be rebuilt at every compile, but not on Win32.
BUILDINFO = $(DSTDIR)/buildinfo
MAKEBUILDINFO = \
	$(RM) $(BUILDINFO).C; \
	echo 'const char *namd_build_date = ' \"`date`\"\; > $(BUILDINFO).C; \
	echo 'const char *namd_build_user = ' \"$(USER)\"\; >> $(BUILDINFO).C; \
	echo 'const char *namd_build_machine = ' \"`hostname`\"\; >> $(BUILDINFO).C; \
	cat $(BUILDINFO).C; \
	$(CXX) $(CXXFLAGS) $(COPTO)$(BUILDINFO).o $(COPTC) $(BUILDINFO).C

all:	$(BINARIES) $(LIBCUDARTSO) $(LIBCUFFTSO)

namd2:	$(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS)
	$(MAKEBUILDINFO)
	$(CHARMC) -verbose -ld++-option \
	'$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)' \
	$(CHARM_MODULES) -language charm++ \
	$(BUILDINFO).o \
	$(OBJS) \
	$(CUDAOBJS) \
	$(CUDALIB) \
	$(DPMTALIB) \
	$(DPMELIB) \
	$(FMMLIB) \
	$(TCLLIB) \
	$(PYTHONLIB) \
	$(FFTLIB) \
	$(PLUGINLIB) \
	$(SBLIB) \
	$(CHARMOPTS) \
	$(EXTRALINKLIBS) \
	-lm -o namd2

charmrun: $(CHARM)/bin/charmrun # XXX
	$(COPY) $(CHARM)/bin/charmrun $@@

$(LIBCUDARTSO):
	$(COPY) $(CUDASODIR)/$(LIBCUDARTSO) $@@;

$(LIBCUFFTSO):
	$(COPY) $(CUDASODIR)/$(LIBCUFFTSO) $@@;

WINDOWSBINARIES = namd2.exe psfgen.exe sortreplicas.exe

winall: $(WINDOWSBINARIES) $(LIBCUDARTSO) $(LIBCUFFTSO)

namd2.exe:  $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) $(TCLDLL)
	$(MAKEBUILDINFO)
	$(CHARMC) -verbose \
	$(CHARM_MODULES) -language charm++ \
	$(BUILDINFO).o \
	$(OBJS) \
	$(CUDAOBJS) \
	$(CUDALIB) \
	$(DPMTALIB) \
	$(DPMELIB) \
	$(FMMLIB) \
	$(TCLLIB) \
	$(PYTHONLIB) \
	$(FFTLIB) \
	$(PLUGINLIB) \
	$(SBLIB) \
	$(CHARMOPTS) \
	-o namd2

charmd.exe:
	$(COPY) $(CHARM)/bin/charmd.exe charmd.exe

charmd_faceless.exe:
	$(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe

charmrun.exe:
	$(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe

psfgen:	$(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS)
	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm

psfgen.exe:	$(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL)
	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm

sortreplicas:	$(MKDSTDIR) $(DSTDIR)/sortreplicas.o $(PLUGINOBJS)
	$(CC) $(SBCFLAGS) -o sortreplicas $(DSTDIR)/sortreplicas.o $(PLUGINOBJS) -lm

sortreplicas.exe:	$(MKDSTDIR) $(DSTDIR)/sortreplicas.o $(PLUGINOBJS)
	$(CC) $(SBCFLAGS) -o sortreplicas $(DSTDIR)/sortreplicas.o $(PLUGINOBJS) -lm

$(DSTDIR)/sortreplicas.o:	$(MKDSTDIR) $(SRCDIR)/sortreplicas.c
	$(CC) $(SBCFLAGS) $(COPTO)$(DSTDIR)/sortreplicas.o $(COPTC) $(SRCDIR)/sortreplicas.c

diffbinpdb:	$(SRCDIR)/diffbinpdb.c
	$(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -lm

flipdcd:	$(SRCDIR)/flipdcd.c
	$(CC) $(CFLAGS) -o $@@ $(SRCDIR)/flipdcd.c || \
	echo "#!/bin/sh\necho unavailable on this platform" > $@@; \
	chmod +x $@@

flipbinpdb:	$(SRCDIR)/flipbinpdb.c
	$(CC) $(CFLAGS) -o $@@ $(SRCDIR)/flipbinpdb.c || \
	echo "#!/bin/sh\necho unavailable on this platform" > $@@; \
	chmod +x $@@

fixdcd:	$(SRCDIR)/fixdcd.c
	$(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c

dumpdcd:	$(SRCDIR)/dumpdcd.c
	$(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c

loaddcd:	$(SRCDIR)/loaddcd.c
	$(CC) $(CFLAGS) -o loaddcd $(SRCDIR)/loaddcd.c

updatefiles:
	touch ../src/ComputeSelfTuples.h
	rm -f obj/ComputeNonbondedPair.o
	rm -f obj/ComputeNonbondedSelf.o
	rm -f obj/ComputePme.o
	rm -f obj/OptPme.o

#To compile tracecomputes, type the command "make tracecomputes TRACEOBJDEF=-DTRACE_COMPUTE_OBJECTS"
tracecomputes: updatefiles $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS)
	$(MAKEBUILDINFO)
	$(CHARMC) -verbose -ld++-option \
	'$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)' \
	$(CHARM_MODULES) -language charm++ \
	-tracemode projections \
	$(BUILDINFO).o \
	$(OBJS) \
	$(CUDAOBJS) \
	$(CUDALIB) \
	$(DPMTALIB) \
	$(DPMELIB) \
	$(FMMLIB) \
	$(TCLLIB) \
	$(PYTHONLIB) \
	$(FFTLIB) \
	$(PLUGINLIB) \
	$(SBLIB) \
	$(CHARMOPTS) \
	$(EXTRALINKLIBS) \
	-lm -o namd2.tc.prj

projections: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS)
	$(MAKEBUILDINFO)
	$(CHARMC) -verbose -ld++-option \
	'$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)' \
	$(CHARM_MODULES) -language charm++ \
	-tracemode projections \
	$(BUILDINFO).o \
	$(OBJS) \
	$(CUDAOBJS) \
	$(CUDALIB) \
	$(DPMTALIB) \
	$(DPMELIB) \
	$(FMMLIB) \
	$(TCLLIB) \
	$(PYTHONLIB) \
	$(FFTLIB) \
	$(PLUGINLIB) \
	$(SBLIB) \
	$(CHARMOPTS) \
	$(EXTRALINKLIBS) \
	-lm -o namd2.prj

summary: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS)
	$(MAKEBUILDINFO)
	$(CHARMC) -verbose -ld++-option \
	'$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)' \
	-module NeighborLB -module CkMulticast -language charm++ \
	-tracemode summary \
	$(BUILDINFO).o \
	$(OBJS) \
	$(CUDAOBJS) \
	$(CUDALIB) \
	$(DPMTALIB) \
	$(DPMELIB) \
	$(FMMLIB) \
	$(TCLLIB) \
	$(PYTHONLIB) \
	$(FFTLIB) \
	$(PLUGINLIB) \
	$(SBLIB) \
	$(CHARMOPTS) \
	$(EXTRALINKLIBS) \
	-lm -o namd2.sum

$(DPMTADIR)/mpole/libmpole.a: $(DPMTADIR)/src/libdpmta2.a

$(DPMTADIR)/src/libdpmta2.a:
	cd $(DPMTADIR) ; $(MAKE) ; cd ..

$(DPMEDIR)/libdpme.a:
	cd $(DPMEDIR) ; $(MAKE) ; cd ..

$(FMMDIR)/src/lib$(FMMNAME).a:
	cd $(FMMDIR) ; $(MAKE) ; cd ..


# Implicit rules for modules.

.SECONDARY:
	# prevent gmake from deleting intermediate files

$(INCDIR)/%.decl.h $(INCDIR)/%.def.h: $(MKINCDIR) $(SRCDIR)/%.ci
	cpp -E -P $(CIPPFLAGS) $(SRCDIR)/$*.ci > $(INCDIR)/$*.ci
	$(CHARMXI) $(INCDIR)/$*.ci
	$(RM) $(INCDIR)/$*.ci
	$(MOVE) $*.def.h $(INCDIR)
	$(MOVE) $*.decl.h $(INCDIR)


# Explicit rules for modules that don't match their file names.
# Multiple targets must be a pattern to execute recipe only once.

$(INCDIR)/PmeFF%Lib.decl.h $(INCDIR)/PmeFF%Lib.def.h: $(MKINCDIR) $(SRCDIR)/fftlib.ci
	$(COPY) $(SRCDIR)/fftlib.ci $(INCDIR)
	$(CHARMXI) $(INCDIR)/fftlib.ci
	$(RM) $(INCDIR)/fftlib.ci
	$(MOVE) PmeFFTLib.def.h $(INCDIR)
	$(MOVE) PmeFFTLib.decl.h $(INCDIR)

$(INCDIR)/OptPm%Mgr.decl.h $(INCDIR)/OptPm%Mgr.def.h: $(MKINCDIR) $(SRCDIR)/OptPme.ci
	$(COPY) $(SRCDIR)/OptPme.ci $(INCDIR)
	$(CHARMXI) $(INCDIR)/OptPme.ci
	$(RM) $(INCDIR)/OptPme.ci
	$(MOVE) OptPmeMgr.def.h $(INCDIR)
	$(MOVE) OptPmeMgr.decl.h $(INCDIR)

DEPENDFILE = .rootdir/Make.depends

# This is a CPU killer...  Don't make depends if you don't need to.
depends: $(MKINCDIR) $(CIFILES) $(MKDSTDIR) $(DEPENDFILE)
	$(ECHO) "Creating " $(DEPENDFILE) " ..."; \
	if [ -f $(DEPENDFILE) ]; then \
	   $(MOVE) -f $(DEPENDFILE) $(DEPENDFILE).old; \
	fi; \
	touch $(DEPENDFILE); \
	for i in $(OBJS) ; do \
	      SRCFILE=$(SRCDIR)/`basename $$i .o`.C ; \
	      COMPILER='$$(CXX)' ; \
	      if [ ! -f $$SRCFILE ]; then \
	            SRCFILE=$(SRCDIR)/`basename $$i .o`.c ; \
	            COMPILER='$$(CC)' ; \
              fi; \
	      $(ECHO) "checking dependencies for $$SRCFILE" ; \
	      g++ -MM $(GXXFLAGS) $$SRCFILE | \
	      perl $(SRCDIR)/dc.pl $(CHARMINC) $(TCLDIR) $(FFTDIR) /usr/include /usr/local $(CUDADIR) >> $(DEPENDFILE); \
	      $(ECHO) '	'$$COMPILER '$$(CXXFLAGS) $$(COPTO)'$$i '$$(COPTC)' \
		$$SRCFILE >> $(DEPENDFILE) ; \
	done; \
	for i in $(CUDAOBJSRAW) ; do \
	      SRCFILE=`basename $$i .o`.cu ; \
	      $(ECHO) "checking dependencies for $(SRCDIR)/$$SRCFILE" ; \
	      g++ -x c++ -MM $(CUDA) $(SRCDIR)/$$SRCFILE | \
	      perl $(SRCDIR)/dc.pl $(CHARMINC) $(TCLDIR) $(FFTDIR) /usr/include /usr/local $(CUDADIR) $(CUBDIR) >> $(DEPENDFILE); \
	      $(ECHO) '	$$(CUDACC) $$(CUDACCOPTS) -Xptxas -v $$(COPTO)'$$i '$$(COPTC)' \
		'`$$(NATIVEPATH) $(SRCDIR)/`'$$SRCFILE >> $(DEPENDFILE) ; \
	done; \
	for i in $(PLUGINOBJS) ; do \
	      BASENAME=`basename $$i .o` ; \
	      SRCFILE=$(PLUGINSRCDIR)/$$BASENAME.c ; \
	      $(ECHO) "checking dependencies for $$SRCFILE" ; \
	      gcc -MM $(PLUGINGCCFLAGS) $$SRCFILE | \
	      perl $(SRCDIR)/dc.pl /usr/include /usr/local >> $(DEPENDFILE); \
	      $(ECHO) '	$$(CC) $$(PLUGINCFLAGS) $$(COPTO)'$$i '$$(COPTC)' \
		'$$(COPTD)'VMDPLUGIN=molfile_$$BASENAME \
		$$SRCFILE >> $(DEPENDFILE) ; \
	done; \
	for i in $(SBOBJS) ; do \
	      SRCFILE=$(SBSRCDIR)/`basename $$i .o`.c ; \
	      $(ECHO) "checking dependencies for $$SRCFILE" ; \
	      gcc -MM $(SBGCCFLAGS) $$SRCFILE | \
	      perl $(SRCDIR)/dc.pl $(CHARMINC) $(TCLDIR) $(FFTDIR) /usr/include /usr/local >> $(DEPENDFILE); \
	      $(ECHO) '	$$(CC) $$(SBCFLAGS) $$(COPTO)'$$i '$$(COPTC)' \
		$$SRCFILE >> $(DEPENDFILE) ; \
	done; \
	$(RM) $(DEPENDFILE).sed; \
	sed -e "/obj\/Controller.o/ s/CXXFLAGS/CXXTHREADFLAGS/" \
	    -e "/obj\/Sequencer.o/ s/CXXFLAGS/CXXTHREADFLAGS/" \
	    -e "/obj\/ComputeFullDirect.o/ s/CXXFLAGS/CXXTHREADFLAGS/" \
	    -e "/obj\/ReductionMgr.o/ s/CXXFLAGS/CXXTHREADFLAGS/" \
	    -e "/obj\/SimParameters.o/ s/CXXFLAGS/CXXSIMPARAMFLAGS/" \
	    -e "/obj\/ComputeNonbondedStd.o/ s/CXXFLAGS/CXXNOALIASFLAGS/" \
	    -e "/obj\/ComputeNonbondedFEP.o/ s/CXXFLAGS/CXXNOALIASFLAGS/" \
	    -e "/obj\/ComputeNonbondedTI.o/ s/CXXFLAGS/CXXNOALIASFLAGS/" \
	    -e "/obj\/ComputeNonbondedLES.o/ s/CXXFLAGS/CXXNOALIASFLAGS/" \
	    -e "/obj\/ComputeNonbondedPProf.o/ s/CXXFLAGS/CXXNOALIASFLAGS/" \
	    -e "/obj\/ComputeNonbondedTabEnergies.o/ s/CXXFLAGS/CXXNOALIASFLAGS/" \
	    -e "/obj\/ComputeNonbondedMIC.o/ s/CXXFLAGS/CXXMICFLAGS/" \
	    -e "/obj\/ComputeNonbondedMICKernel.o/ s/CXXFLAGS/CXXMICFLAGS/" \
	    -e "/obj\/colvar.*.o/ s/CXXFLAGS/CXXCOLVARFLAGS/" \
	    -e "/obj\/memusage.o/ s/CXX/CXXMEMUSAGE/" \
	    $(DEPENDFILE) > $(DEPENDFILE).sed; \
	$(MOVE) -f $(DEPENDFILE).sed $(DEPENDFILE);

$(DEPENDFILE):
	touch $(DEPENDFILE)

include Make.depends

$(MKDSTDIR):
	if [ ! -d $(DSTDIR) ]; then $(MKDIR) $(DSTDIR); fi
	if [ ! -f $(MKDSTDIR) ]; then touch $(MKDSTDIR); fi

$(MKINCDIR):
	if [ ! -d $(INCDIR) ]; then $(MKDIR) $(INCDIR); fi
	if [ ! -f $(MKINCDIR) ]; then touch $(MKINCDIR); fi

clean:
	rm -rf ptrepository Templates.DB SunWS_cache $(DSTDIR) $(INCDIR)

veryclean:	clean
	rm -f $(BINARIES)

RELEASE_DIR_NAME = NAMD_$(NAMD_VERSION)_$(NAMD_PLATFORM)

DOC_FILES = README.txt announce.txt license.txt notes.txt

RELEASE_FILES = $(LIBCUDARTSO) $(LIBCUFFTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2

WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(LIBCUFFTSO) $(WINDOWSBINARIES) $(TCLDLL)

release: all
	$(ECHO) Creating release $(RELEASE_DIR_NAME)
	mkdir $(RELEASE_DIR_NAME)
	cp $(RELEASE_FILES) $(COMPILERRUNTIMELIBS) $(RELEASE_DIR_NAME)
	for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done
	cp -r .rootdir/lib $(RELEASE_DIR_NAME)
	for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \
	  /bin/rm -rf $$f; \
	done
	if [ -r $(CHARM)/bin/charmd ]; then \
	  $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
	fi
	if [ -r $(CHARM)/bin/charmd_faceless ]; then \
	  $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
	fi
	chmod -R a+rX $(RELEASE_DIR_NAME)
	tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
	gzip $(RELEASE_DIR_NAME).tar
	echo $(CHARM)
	ls -l $(CHARM)/lib
	-for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done

winrelease: winall
	$(ECHO) Creating release $(RELEASE_DIR_NAME)
	mkdir $(RELEASE_DIR_NAME)
	cp $(WINDOWS_RELEASE_FILES) $(RELEASE_DIR_NAME)
	for f in $(DOC_FILES); do \
	  perl -p -i -e 's/(?<!\r)\n$$/\r\n/' < .rootdir/$$f > $(RELEASE_DIR_NAME)/$$f; \
	done
	cp -r .rootdir/lib $(RELEASE_DIR_NAME)
	for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \
	  /bin/rm -rf $$f; \
	done
	for f in `find $(RELEASE_DIR_NAME)/lib -type f`; do \
	  perl -p -i -e 's/(?<!\r)\n$$/\r\n/' < $$f > $$f.wintxt; \
	  mv $$f.wintxt $$f; \
	done
	chmod -R a+rX $(RELEASE_DIR_NAME)
	echo $(CHARM)
	ls -l $(CHARM)/lib
	echo $(CHARM)
	zip -r $(RELEASE_DIR_NAME).zip $(RELEASE_DIR_NAME)

@


1.1360
log
@Build NAMD .c files with $(CC) instead of $(CXX), but still use $(CXXFLAGS)
@
text
@d69 1
a69 1
EXTRADEFINES=-DREMOVE_PROXYRESULTMSG_EXTRACOPY -DNODEAWARE_PROXY_SPANNINGTREE -DUSE_NODEPATCHMGR
d139 1
d195 1
d392 1
d398 1
a398 2
	$(DSTDIR)/CudaTileListKernel.o \
	$(DSTDIR)/DeviceCUDAkernel.o
d455 1
a455 1
CIPPFLAGS = $(CUDAFLAGS)
@


1.1359
log
@Support CUDA 8.0, which requires different gencode options to dlink cuFFT static library.
@
text
@d697 1
d700 1
d705 1
a705 1
	      $(ECHO) '	$$(CXX) $$(CXXFLAGS) $$(COPTO)'$$i '$$(COPTC)' \
@


1.1358
log
@Update to 2.12.
@
text
@d402 1
a402 1
	$(CUDACC) $(CUDACCOPTS) -v -lcufft_static -dlink $(DSTDIR)/CudaPmeSolverUtilKernel.o $(COPTO)$@@
@


1.1357
log
@Update to 2.12b1.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.12b1
@


1.1356
log
@Colvars update from Giacomo Fiorin and Jerome Henin.
- Parallel calculation of center-of-mass based variables
- Shared-memory parallel calculation of many variables (requires CkLoop)
- Change in ABF convention: PLEASE SEE http://colvars.github.io/README-totalforce.md
- Extended-system ABF method by the CZAR estimator
- Histogram calculation on ensembles of variables, with optional weights
- Probability distribution restraints
- Contributed variable types: dipoleAngle (Alejandro Bernardin), groupCoordNum (Alan Grossfield)
- Scripting command "cvcflags" to optimize performance of complex colvars
- Scripting commands getappliedforce to gettotalforce to implement thermodynamic integration-based methods
- Improved error handling in user input and Tcl scripts
@
text
@d2 1
a2 1
NAMD_VERSION = 2.11
@


1.1355
log
@QM/MM interface from Marcelo Melo.
@
text
@d236 1
@


1.1354
log
@Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot.
@
text
@d151 1
d258 1
d344 2
@


1.1353
log
@New CUDA kernels and PME from Antti-Pekka Hynninen.  Enable with "useCUDA2 yes" and "usePMECUDA yes".
@
text
@d115 4
@


1.1352
log
@Add --with-python option to build optional Python interface.
@
text
@d138 1
d177 2
d188 3
d270 1
d318 2
d326 4
d334 2
d381 1
d383 5
a387 1
	$(DSTDIR)/ComputeNonbondedCUDAKernel.o
d389 5
a393 11
$(DSTDIR)/ComputePmeCUDAKernel.o: \
	$(SRCDIR)/ComputePmeCUDAKernel.cu \
	$(SRCDIR)/ComputePmeCUDAKernel.h
	$(CUDACC) $(CUDACCOPTS) -Xptxas -v $(COPTO) "`$(NATIVEPATH) $(DSTDIR)/`ComputePmeCUDAKernel.o" $(COPTC) "`$(NATIVEPATH) $(SRCDIR)/`ComputePmeCUDAKernel.cu"

$(DSTDIR)/ComputeNonbondedCUDAKernel.o: \
	$(SRCDIR)/ComputeNonbondedCUDAKernel.cu \
	$(SRCDIR)/ComputeNonbondedCUDAKernelBase.h \
	$(SRCDIR)/ComputeGBISCUDAKernel.h \
	$(SRCDIR)/ComputeNonbondedCUDAKernel.h
	$(CUDACC) $(CUDACCOPTS) -Xptxas -v $(COPTO) "`$(NATIVEPATH) $(DSTDIR)/`ComputeNonbondedCUDAKernel.o" $(COPTC) "`$(NATIVEPATH) $(SRCDIR)/`ComputeNonbondedCUDAKernel.cu"
d443 3
d460 1
a460 1
all:	$(BINARIES) $(LIBCUDARTSO)
d489 3
d494 1
a494 1
winall: $(WINDOWSBINARIES) $(LIBCUDARTSO)
d653 1
a653 1
	$(COPY) $(SRCDIR)/$*.ci $(INCDIR)
d693 1
a693 1
	      perl $(SRCDIR)/dc.pl $(CHARMINC) $(TCLDIR) $(FFTDIR) /usr/include /usr/local >> $(DEPENDFILE); \
d697 8
d765 1
a765 1
RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2
d767 1
a767 1
WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL)
@


1.1351
log
@Fix MIC build by limiting MIC offload options to files that need them.
@
text
@d415 1
a415 1
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(FMM) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(FFT) $(CUDA) $(MIC) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS) $(MSA) $(CKLOOP)
d458 1
d488 1
d563 1
d585 1
d607 1
@


1.1350
log
@Enable AVX vectorization with Intel compiler while also running on earlier processors.
Disable for colvars due to reference defined in discarded section errors with -axAVX.
@
text
@d416 6
a421 5
CXXFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) $(CXXMICOPTS)
CXXTHREADFLAGS = $(CXXBASEFLAGS) $(CXXTHREADOPTS) $(CXXMICOPTS)
CXXSIMPARAMFLAGS = $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS) $(CXXMICOPTS)
CXXNOALIASFLAGS = $(CXXBASEFLAGS) $(CXXNOALIASOPTS) $(CXXMICOPTS)
CXXCOLVARFLAGS = $(CXXBASEFLAGS) $(CXXCOLVAROPTS) $(CXXMICOPTS)
d448 1
a448 1
	'$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS) $(CXXMICOPTS)' \
d550 1
a550 1
	'$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS) $(CXXMICOPTS)' \
d571 1
a571 1
	'$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS) $(CXXMICOPTS)' \
d592 1
a592 1
	'$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS) $(CXXMICOPTS)' \
d702 2
@


1.1349
log
@Update to 2.11.
@
text
@d87 1
d420 1
d701 1
@


1.1348
log
@Update to 2.11b2.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.11b2
@


1.1347
log
@Update to 2.11b1.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.11b1
@


1.1346
log
@Link psfgen module statically in NAMD - use "package require psfgen" to enable.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.10
@


1.1345
log
@Disable CkLoop for Win64 builds.
@
text
@d380 3
a382 2
SBOBJS = \
	$(DSTDIR)/tcl_main.o \
d411 1
a411 1
LIBS = $(CUDAOBJS) $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(FMMLIBS) $(TCLDLL)
d457 1
d486 1
d560 1
d581 1
d602 1
@


1.1344
log
@Major update to collective variables module from Giacomo Fiorin and Jerome Henin: Tcl scripts to expand existing functionality, improvements to histogram bias, colvarsConfig is now optional ("cv" command), and bug fixes.
@
text
@d78 5
d404 1
a404 1
CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -module CkMulticast -module CkLoop
a407 3
#If using the CkLoop library from Charm++ for PME calculation, first define macro
# USE_CKLOOP=1 for compiling the code, and then add "-module CkLoop" for linking.
CKLOOP = -DUSE_CKLOOP=1
@


1.1343
log
@CUDA optimization and refactoring from Antti-Pekka Hynninen.
@
text
@d210 1
@


1.1342
log
@Enable use of CkLoop library.
@
text
@d179 1
d182 1
@


1.1341
log
@Increase version to 2.10.
@
text
@d396 1
a396 1
CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -module CkMulticast
d402 1
d408 1
a408 1
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(FMM) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(FFT) $(CUDA) $(MIC) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS) $(MSA)
d440 1
a440 1
	"$(CHARM_MODULES)" -language charm++ \
d468 1
a468 1
	-module NeighborLB -module CkMulticast -language charm++ \
d540 1
a540 1
	-module NeighborLB -module CkMulticast -language charm++ \
d560 1
a560 1
	-module NeighborLB -module CkMulticast -language charm++ \
@


1.1340
log
@Add new ofstream_namd class with std::ofstream interface to handle interrupted system calls an other error checking.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.10b2
@


1.1339
log
@Increase version to 2.10b2.
@
text
@d190 1
@


1.1338
log
@Massive colvars updates from Jerome Henin and Giacomo Fiorin:
 - multiple-walker ABF by Jeff Comer and Chris Chipot,
 - Adaptive Linear Bias by Andrew White (Voth group),
 - Tcl-scripted colvars and biases (docs commented out for now).
@
text
@d2 1
a2 1
NAMD_VERSION = 2.10b1
@


1.1337
log
@updates for 2.10b1 release
@
text
@a201 2
	$(DSTDIR)/colvarmodule.o \
	$(DSTDIR)/colvarparse.o \
d203 1
a203 1
	$(DSTDIR)/colvarvalue.o \
d206 1
d208 1
a208 1
	$(DSTDIR)/colvaratoms.o \
d215 3
d219 3
a221 1
	$(DSTDIR)/colvargrid.o \
@


1.1336
log
@Offload PME charge gridding and force interpolation to GPU. Controlled by PMEOffload param with default off for PMEInterpOrder 4 (default) and on for PMEInterpOrder > 4 (useful for petascale runs).
@
text
@d2 1
a2 1
NAMD_VERSION = 2.9
@


1.1335
log
@New Go GromacsPair implementation from Jonathan Lai.
@
text
@d352 1
d354 5
@


1.1334
log
@Port to Intel Xeon Phi "MIC" accelerator by David M. Kunzman of Intel.
@
text
@d142 1
@


1.1333
log
@Add CXXMEMUSAGE macro to select compiler for memusage.C.
@
text
@d164 2
d395 5
a399 5
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(FMM) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(FFT) $(CUDA) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS) $(MSA)
CXXFLAGS = $(CXXBASEFLAGS) $(CXXOPTS)
CXXTHREADFLAGS = $(CXXBASEFLAGS) $(CXXTHREADOPTS)
CXXSIMPARAMFLAGS = $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS)
CXXNOALIASFLAGS = $(CXXBASEFLAGS) $(CXXNOALIASOPTS)
d426 1
a426 1
	"$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
d526 1
a526 1
	"$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
d546 1
a546 1
	"$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
d566 1
a566 1
	"$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
@


1.1332
log
@Compile memusage.C with charmc to enable BG/Q kernel include paths.
@
text
@d82 1
d673 1
a673 1
	    -e "/obj\/memusage.o/ s/CXX/CHARMC/" \
@


1.1331
log
@Added serial interface for external FMM library.
Can be specifically used with ufmmlap.
@
text
@d672 1
@


1.1330
log
@Do not include summary in projections builds.
@
text
@d49 15
d98 1
d285 2
d389 1
a389 1
LIBS = $(CUDAOBJS) $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL)
d392 1
a392 1
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(FFT) $(CUDA) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS) $(MSA)
d431 1
d459 1
d532 1
d552 1
d572 1
d587 3
@


1.1329
log
@Nikhil Jain's modification of Tcl replica functions to use new partition
capability in Charm++ 6.5.0 for mpi, gemini_gni, and pamilrts builds
(and any future platform based on the lrts common runtime implementation).
No changes to the behavior of Tcl replica functions are expected.
@
text
@d524 1
a524 1
	-tracemode projections -tracemode summary \
@


1.1328
log
@Fix missing cuda runtime dll on Windows.
@
text
@d254 1
d313 2
@


1.1327
log
@Added module for Charm++ CkMulticast and regenerated dependencies.
@
text
@d424 2
a425 2
# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
windowsbinaries: $(WINDOWSBINARIES)
@


1.1326
log
@PME optimizations via template specialization, inlining, __restrict, etc.
@
text
@d360 2
a361 1
CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
d430 1
a430 1
	-module NeighborLB -language charm++ \
d501 1
a501 1
	-module NeighborLB -language charm++ \
d520 1
a520 1
	-module NeighborLB -language charm++ \
d539 1
a539 1
	-module NeighborLB -language charm++ \
@


1.1325
log
@Reorder to avoid multiply including Make.config.
@
text
@a227 1
	$(DSTDIR)/PmeBase.o \
@


1.1324
log
@fixes for compilation errors on BG/Q
@
text
@d10 1
a10 1
include Make.config
d12 6
a17 2
# define below Make.config so Win32 can change default target to winall
default: all
d73 3
a561 11
# Unix commands

ECHO = echo
MOVE = mv
MKDIR = mkdir -p
COPY = cp
RM = rm -f
LDD = ldd

include Make.config

@


1.1323
log
@Added a comment on how to compile NAMD when using the CkLoop library
@
text
@d378 1
a378 1
BINARIES = namd2 psfgen sortreplicas charmrun flipdcd flipbinpdb
@


1.1322
log
@Add --with-spec option to add warning and disable dcd output for SPEC release.
@
text
@d357 2
@


1.1321
log
@Build files for new MSM
@
text
@d16 1
a16 1
RELEASE=$(COPTD)NAMD_VERSION=\"$(NAMD_VERSION)\" $(COPTD)NAMD_PLATFORM=\"$(NAMD_PLATFORM)\" $(SCYLDFLAGS)
@


1.1320
log
@Update to version 2.9.
@
text
@d73 1
d256 2
@


1.1319
log
@Update to version 2.9b3.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.9b3
@


1.1318
log
@Changed ComputeMsm to ComputeMsmMsa along with related names.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.9b2
@


1.1317
log
@Version 2.9b2.
@
text
@d73 1
a73 1
	$(DSTDIR)/ComputeMsm.o \
d255 2
a256 2
		$(INCDIR)/ComputeMsmMgr.decl.h \
		$(INCDIR)/ComputeMsmMgr.def.h \
@


1.1316
log
@Fix MOA build.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.9b1
@


1.1315
log
@Generating ptx code doesn't work with multiple device code generation.
@
text
@d72 1
@


1.1314
log
@Update docs/notes/announcement and bump version to 2.9b1.
@
text
@a323 2
	$(CUDACC) -ptx "`$(NATIVEPATH) $(SRCDIR)/`ComputeNonbondedCUDAKernel.cu"
	grep global ComputeNonbondedCUDAKernel.ptx
@


1.1313
log
@Fix build with stub files includes.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.8
@


1.1312
log
@linear combination of pairwise overlaps (LCPO) for solvent accessible surface area (SASA) calculation to accompany GBIS implicit solvent
@
text
@d252 2
@


1.1311
log
@Go forces implementation from Jonathan Lai.
@
text
@d116 1
@


1.1310
log
@Change -e to -f in file existence test to support sh on Solaris.
@
text
@d130 1
d202 1
@


1.1309
log
@Add -DNODEAWARE_PROXY_SPANNINGTREE -DUSE_NODEPATCHMGR
@
text
@d648 1
a648 1
	if [ ! -e $(MKDSTDIR) ]; then touch $(MKDSTDIR); fi
d652 1
a652 1
	if [ ! -e $(MKINCDIR) ]; then touch $(MKINCDIR); fi
@


1.1308
log
@Eliminate spurious re-linking by depending on obj/.exists instead of obj.
@
text
@d50 1
a50 2
#EXTRADEFINES=-DREMOVE_PROXYRESULTMSG_EXTRACOPY -DNODEAWARE_PROXY_SPANNINGTREE
EXTRADEFINES=-DREMOVE_PROXYRESULTMSG_EXTRACOPY 
@


1.1307
log
@Fix Windows builds of sortreplicas.
@
text
@d28 3
d384 1
a384 1
namd2:	$(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
d412 1
a412 1
namd2.exe:  $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) $(TCLDLL)
d437 1
a437 1
psfgen:	$(DSTDIR) $(SBOBJS) $(PLUGINOBJS)
d440 1
a440 1
psfgen.exe:	$(DSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL)
d443 1
a443 1
sortreplicas:	$(DSTDIR) $(DSTDIR)/sortreplicas.o $(PLUGINOBJS)
d446 1
a446 1
sortreplicas.exe:	$(DSTDIR) $(DSTDIR)/sortreplicas.o $(PLUGINOBJS)
d449 1
a449 1
$(DSTDIR)/sortreplicas.o:	$(DSTDIR) $(SRCDIR)/sortreplicas.c
d482 1
a482 1
tracecomputes: updatefiles $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
d501 1
a501 1
projections: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
d520 1
a520 1
summary: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
d564 1
a564 2
$(INCDIR)/%.decl.h $(INCDIR)/%.def.h: $(SRCDIR)/%.ci
	$(MKDIR) $(INCDIR)
d575 1
a575 2
$(INCDIR)/PmeFF%Lib.decl.h $(INCDIR)/PmeFF%Lib.def.h: $(SRCDIR)/fftlib.ci
	$(MKDIR) $(INCDIR)
d582 1
a582 2
$(INCDIR)/OptPm%Mgr.decl.h $(INCDIR)/OptPm%Mgr.def.h: $(SRCDIR)/OptPme.ci
	$(MKDIR) $(INCDIR)
d592 1
a592 1
depends: $(INCDIR) $(CIFILES) $(DSTDIR) $(DEPENDFILE)
d647 7
a653 5
$(DSTDIR):
	$(MKDIR) $(DSTDIR)

$(INCDIR):
	$(MKDIR) $(INCDIR)
@


1.1306
log
@Add new sortreplicas program to un-shuffle replica-exchange trajectories.
@
text
@d440 2
a441 2
sortreplicas:	$(DSTDIR) $(SRCDIR)/sortreplicas.c $(PLUGINOBJS)
	$(CC) $(SBCFLAGS) -o sortreplicas $(SRCDIR)/sortreplicas.c $(PLUGINOBJS) -lm
d443 5
a447 2
sortreplicas.exe:	$(DSTDIR) $(SRCDIR)/sortreplicas.c $(PLUGINOBJS)
	$(CC) $(SBCFLAGS) -o sortreplicas $(SRCDIR)/sortreplicas.c $(PLUGINOBJS) -lm
@


1.1305
log
@adding CUDA support for GBIS
@
text
@d367 1
a367 1
BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb
d405 1
a405 1
WINDOWSBINARIES = namd2.exe psfgen.exe
d440 6
d660 1
a660 1
RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen charmrun namd2
@


1.1304
log
@Include new file ComputeNonbondedCUDAKernelBase.h as dependency for
ComputeNonbondedCUDAKernel.o.
@
text
@d315 1
d319 1
a319 1
	$(CUDACC) -Xptxas -v $(COPTO) "`$(NATIVEPATH) $(DSTDIR)/`ComputeNonbondedCUDAKernel.o" $(COPTC) "`$(NATIVEPATH) $(SRCDIR)/`ComputeNonbondedCUDAKernel.cu"
@


1.1303
log
@build parallel MSM using Charm MSA module
@
text
@d314 1
@


1.1302
log
@had to take out msa module, not yet included in Jim's charm++ builds
@
text
@d70 1
d247 2
d343 3
d351 1
a351 1
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(FFT) $(CUDA) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS)
d383 1
a383 1
	-module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -language charm++ \
@


1.1301
log
@Building serial version of MSM long-range calculation.
@
text
@d377 1
a377 1
	-module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -language charm++ \
@


1.1300
log
@Update version to 2.8.
@
text
@d70 8
d246 2
d377 1
a377 1
	-module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -language charm++ \
d583 3
@


1.1299
log
@Update version to 2.8b3.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.8b3
@


1.1298
log
@Use CXXNOALIASFLAGS on more ComputeNonbonded... main loop files.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.8b2
@


1.1297
log
@Update version to 2.8b2.
@
text
@d605 1
d607 2
@


1.1296
log
@Add CUDA runtime DLL to Windows release file list.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.8b1
@


1.1295
log
@Add CUDA support for Win64 and MacOSX-x86_64.
@
text
@d632 1
a632 1
WINDOWS_RELEASE_FILES = $(WINDOWSBINARIES) $(TCLDLL)
@


1.1294
log
@Removed the redundant explanation of compiling node-aware proxy spanning tree
@
text
@d63 1
d302 1
a302 1
	$(CUDACC) -ptx $(SRCDIR)/ComputeNonbondedCUDAKernel.cu
d304 1
a304 1
	$(CUDACC) -Xptxas -v $(COPTO)$(DSTDIR)/ComputeNonbondedCUDAKernel.o $(COPTC) $(SRCDIR)/ComputeNonbondedCUDAKernel.cu
d385 1
a385 5
	if [ -r $(CUDADIR)/lib64/$(LIBCUDARTSO) ]; then \
	  $(COPY) $(CUDADIR)/lib64/$(LIBCUDARTSO) $@@; \
	else \
	  $(COPY) $(CUDADIR)/lib/$(LIBCUDARTSO) $@@; \
	fi
@


1.1293
log
@Remove the explanation of using plain 2-level node-aware spanning tree.
Replaced it with the general node-aware spanning tree.
@
text
@d44 1
a44 3
# to compile version that uses node aware spanning tree, add 
#-DNODEAWARE_PROXY_SPANNINGTREE to the variable EXTRADEFINES
# to compile version that uses node-aware proxy send/recv,
@


1.1292
log
@Added the macro to define when to use the simple plain node-aware proxy
send/recv scheme (a simple two-level tree)
@
text
@d46 2
a47 2
# to compile version that uses plain node-aware proxy send/recv (2-level tree),
# add -DUSE_TWOLEVEL_PROXY_SENDRECV to the variable EXTRADEFINES
d49 1
@


1.1291
log
@Update versions to 2.8b1.
@
text
@d44 4
a47 2
# to compile version that uses node aware spanning tree, add -DNODEAWARE_PROXY_SPANNINGTREE
# to the variable EXTRADEFINES
d49 1
a49 1
EXTRADEFINES=-DREMOVE_PROXYRESULTMSG_EXTRACOPY
@


1.1290
log
@Don't try to pre-process .ci files.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.7
@


1.1289
log
@Add diffbinpdb target.
@
text
@d325 1
a325 1
CHARMXI = $(CHARM)/bin/charmc -E $(EXTRADEFINES)
@


1.1288
log
@Added support to compile namd with PAPI library
@
text
@d424 3
@


1.1287
log
@Break thermodynamics integration out into ComputeNonbondedTI.C to reduce
compile time for ComputeNonbondedFEP.C.
@
text
@d47 8
a54 1
EXTRADEFINES=-DREMOVE_PROXYRESULTMSG_EXTRACOPY 
d325 1
a325 1
CHARMXI = $(CHARM)/bin/charmc
d333 1
a333 1
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(FFT) $(CUDA) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
d376 1
d467 1
d486 1
d505 1
@


1.1286
log
@Add namdbin plugin.
@
text
@d110 1
@


1.1285
log
@First Domain and Symmetry Restraint commit
@
text
@d280 1
@


1.1284
log
@Adding GBIS (Generalized Born Implicit Solvent) by David Tanner
@
text
@d145 2
@


1.1283
log
@Changes due to removing unnecessary files as AtomsDisInfo.* and FileIO*
@
text
@d94 2
d244 2
a544 1

@


1.1282
log
@Update version to 2.7.
@
text
@d218 1
a218 3
	$(DSTDIR)/ParallelIOMgr.o \
	$(DSTDIR)/AtomsDisInfo.o \
	$(DSTDIR)/FileIO.o 
d267 1
a267 5
		$(INCDIR)/main.def.h \
		$(INCDIR)/AtomsDisInfo.decl.h \
		$(INCDIR)/AtomsDisInfo.def.h \
		$(INCDIR)/FileIO.decl.h \
		$(INCDIR)/FileIO.def.h
@


1.1281
log
@Update version to 2.7b4.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.7b4
@


1.1280
log
@Better handling of COMPILERRUNTIMELIBS and ldd in make release.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.7b3
@


1.1279
log
@ship libstlport with NAMD binary
@
text
@d617 1
a617 1
RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen charmrun namd2 $(COMPILERRUNTIMELIBS)
d624 1
a624 1
	cp $(RELEASE_FILES) $(RELEASE_DIR_NAME)
d641 1
a641 1
	-for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done
@


1.1278
log
@Use pattern with multiple targets to build .decl.h and .def.h in one rule.
@
text
@d617 1
a617 1
RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen charmrun namd2
@


1.1277
log
@Use .SECONDARY target to prevent gmake from deleting intermediate files
@
text
@d520 1
a520 4
$(INCDIR)/%.decl.h: $(INCDIR)/%.def.h
	# .decl.h file built by .def.h rule

$(INCDIR)/%.def.h: $(SRCDIR)/%.ci
d530 1
d532 1
a532 4
$(INCDIR)/PmeFFTLib.decl.h: $(INCDIR)/PmeFFTLib.def.h
	# .decl.h file built by .def.h rule

$(INCDIR)/PmeFFTLib.def.h: $(SRCDIR)/fftlib.ci
d540 1
a540 4
$(INCDIR)/OptPmeMgr.decl.h: $(INCDIR)/OptPmeMgr.def.h
	# .decl.h file built by .def.h rule

$(INCDIR)/OptPmeMgr.def.h: $(SRCDIR)/OptPme.ci
@


1.1276
log
@Use mkdir -p (via MKDIR macro) to not die on parallel make race condition.
@
text
@d517 3
@


1.1275
log
@mkdir -p inc in recipies to eliminate race condition on gmake -j 128 etc.
@
text
@d607 1
a607 1
	mkdir $(DSTDIR)
d610 1
a610 1
	mkdir $(INCDIR)
@


1.1274
log
@Reorder since .decl.h file is written slightly later than .def.h file.
@
text
@d507 1
d521 1
d535 1
d546 1
@


1.1273
log
@updating NAMD and Charm++ versions.
@
text
@d516 2
a517 2
$(INCDIR)/%.def.h: $(INCDIR)/%.decl.h
	$(ECHO) remove $(INCDIR)/$*.decl.h and re-build
d519 1
a519 1
$(INCDIR)/%.decl.h: $(SRCDIR)/%.ci
d529 2
a530 2
$(INCDIR)/PmeFFTLib.def.h: $(INCDIR)/PmeFFTLib.decl.h
	$(ECHO) remove $(INCDIR)/$*.decl.h and re-build
d532 1
a532 1
$(INCDIR)/PmeFFTLib.decl.h: $(SRCDIR)/fftlib.ci
d539 2
a540 2
$(INCDIR)/OptPmeMgr.def.h: $(INCDIR)/OptPmeMgr.decl.h
	$(ECHO) remove $(INCDIR)/$*.decl.h and re-build
d542 1
a542 1
$(INCDIR)/OptPmeMgr.decl.h: $(SRCDIR)/OptPme.ci
@


1.1272
log
@Use echo to keep parallel make happy and advise user about .def.h files.
(The .def.h file is created by the same command as the .decl.h file.)
@
text
@d2 1
a2 1
NAMD_VERSION = 2.7b2
@


1.1271
log
@ParallelIO Checkin
@
text
@d517 1
d530 1
d540 1
@


1.1270
log
@Remove Charm++ communications library.
@
text
@d218 1
d266 2
@


1.1269
log
@Put nvcc as last command in rule so that make dies if nvcc fails.
@
text
@d353 1
a353 1
	-module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -module commlib -language charm++ \
d383 1
a383 1
	-module NeighborLB -module commlib -language charm++ \
d442 1
a442 1
	-module NeighborLB -module commlib -language charm++ \
d460 1
a460 1
	-module NeighborLB -module commlib -language charm++ \
d478 1
a478 1
	-module NeighborLB -module commlib -language charm++ \
@


1.1268
log
@Finished infrastructure for calculating anisotropic Drude harmonic potential
@
text
@a287 1
	$(CUDACC) -Xptxas -v $(COPTO)$(DSTDIR)/ComputeNonbondedCUDAKernel.o $(COPTC) $(SRCDIR)/ComputeNonbondedCUDAKernel.cu
d290 1
@


1.1267
log
@Added ComputeThole.
@
text
@d81 1
@


1.1266
log
@Added SortAtoms.C and SortAtoms.h, some changes due to format diffs.
@
text
@d121 1
@


1.1265
log
@Syntax fix.
@
text
@d205 1
@


1.1264
log
@Copy and convert entire lib directory in make winrelease (was in config).
@
text
@d619 1
a619 1
	for f in `find (RELEASE_DIR_NAME)/lib -name CVS`; do \
@


1.1263
log
@Fix .ci file rules to avoid copying src directory on Windows.
@
text
@d619 3
a621 1
	/bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS
d638 12
a649 2
	cp $(DOC_FILES) $(WINDOWS_RELEASE_FILES) $(RELEASE_DIR_NAME)
	cp -r lib $(RELEASE_DIR_NAME)
@


1.1262
log
@*** empty log message ***
@
text
@d219 1
a219 1
# Add new modules here and also define explicit rule below.
a506 1
# Explicit rules for modules.
d508 1
a508 1
$(INCDIR)/BroadcastMgr.def.h: $(INCDIR)/BroadcastMgr.decl.h
d510 1
a510 4
$(INCDIR)/BroadcastMgr.decl.h: $(SRCDIR)/BroadcastMgr.ci
	$(CHARMXI) $(SRCDIR)/BroadcastMgr.ci
	$(MOVE) BroadcastMgr.def.h $(INCDIR)
	$(MOVE) BroadcastMgr.decl.h $(INCDIR)
d512 6
a517 1
$(INCDIR)/CollectionMaster.def.h: $(INCDIR)/CollectionMaster.decl.h
a518 4
$(INCDIR)/CollectionMaster.decl.h: $(SRCDIR)/CollectionMaster.ci
	$(CHARMXI) $(SRCDIR)/CollectionMaster.ci
	$(MOVE) CollectionMaster.def.h $(INCDIR)
	$(MOVE) CollectionMaster.decl.h $(INCDIR)
d520 1
a520 6
$(INCDIR)/CollectionMgr.def.h: $(INCDIR)/CollectionMgr.decl.h

$(INCDIR)/CollectionMgr.decl.h: $(SRCDIR)/CollectionMgr.ci
	$(CHARMXI) $(SRCDIR)/CollectionMgr.ci
	$(MOVE) CollectionMgr.def.h $(INCDIR)
	$(MOVE) CollectionMgr.decl.h $(INCDIR)
d525 3
a527 1
	$(CHARMXI) $(SRCDIR)/fftlib.ci
a530 21
$(INCDIR)/ComputeMgr.def.h: $(INCDIR)/ComputeMgr.decl.h

$(INCDIR)/ComputeMgr.decl.h: $(SRCDIR)/ComputeMgr.ci
	$(CHARMXI) $(SRCDIR)/ComputeMgr.ci
	$(MOVE) ComputeMgr.def.h $(INCDIR)
	$(MOVE) ComputeMgr.decl.h $(INCDIR)

$(INCDIR)/ComputePmeMgr.def.h: $(INCDIR)/ComputePmeMgr.decl.h

$(INCDIR)/ComputePmeMgr.decl.h: $(SRCDIR)/ComputePmeMgr.ci
	$(CHARMXI) $(SRCDIR)/ComputePmeMgr.ci
	$(MOVE) ComputePmeMgr.def.h $(INCDIR)
	$(MOVE) ComputePmeMgr.decl.h $(INCDIR)

$(INCDIR)/ComputeGridForceMgr.def.h: $(INCDIR)/ComputeGridForceMgr.decl.h

$(INCDIR)/ComputeGridForceMgr.decl.h: $(SRCDIR)/ComputeGridForceMgr.ci
	$(CHARMXI) $(SRCDIR)/ComputeGridForceMgr.ci
	$(MOVE) ComputeGridForceMgr.def.h $(INCDIR)
	$(MOVE) ComputeGridForceMgr.decl.h $(INCDIR)

d534 3
a536 1
	$(CHARMXI) $(SRCDIR)/OptPme.ci
a538 105

$(INCDIR)/ComputeExtMgr.def.h: $(INCDIR)/ComputeExtMgr.decl.h

$(INCDIR)/ComputeExtMgr.decl.h: $(SRCDIR)/ComputeExtMgr.ci
	$(CHARMXI) $(SRCDIR)/ComputeExtMgr.ci
	$(MOVE) ComputeExtMgr.def.h $(INCDIR)
	$(MOVE) ComputeExtMgr.decl.h $(INCDIR)

$(INCDIR)/LdbCoordinator.def.h: $(INCDIR)/LdbCoordinator.decl.h

$(INCDIR)/LdbCoordinator.decl.h: $(SRCDIR)/LdbCoordinator.ci
	$(CHARMXI) $(SRCDIR)/LdbCoordinator.ci
	$(MOVE) LdbCoordinator.def.h $(INCDIR)
	$(MOVE) LdbCoordinator.decl.h $(INCDIR)

$(INCDIR)/NamdCentLB.def.h: $(INCDIR)/NamdCentLB.decl.h

$(INCDIR)/NamdCentLB.decl.h: $(SRCDIR)/NamdCentLB.ci
	$(CHARMXI) $(SRCDIR)/NamdCentLB.ci
	$(MOVE) NamdCentLB.def.h $(INCDIR)
	$(MOVE) NamdCentLB.decl.h $(INCDIR)

$(INCDIR)/NamdNborLB.def.h: $(INCDIR)/NamdNborLB.decl.h

$(INCDIR)/NamdNborLB.decl.h: $(SRCDIR)/NamdNborLB.ci
	$(CHARMXI) $(SRCDIR)/NamdNborLB.ci
	$(MOVE) NamdNborLB.def.h $(INCDIR)
	$(MOVE) NamdNborLB.decl.h $(INCDIR)

$(INCDIR)/NamdHybridLB.def.h: $(INCDIR)/NamdHybridLB.decl.h

$(INCDIR)/NamdDummyLB.def.h: $(INCDIR)/NamdDummyLB.decl.h

$(INCDIR)/NamdHybridLB.decl.h: $(SRCDIR)/NamdHybridLB.ci
	$(CHARMXI) $(SRCDIR)/NamdHybridLB.ci
	$(MOVE) NamdHybridLB.def.h $(INCDIR)
	$(MOVE) NamdHybridLB.decl.h $(INCDIR)

$(INCDIR)/NamdDummyLB.decl.h: $(SRCDIR)/NamdDummyLB.ci
	$(CHARMXI) $(SRCDIR)/NamdDummyLB.ci
	$(MOVE) NamdDummyLB.def.h $(INCDIR)
	$(MOVE) NamdDummyLB.decl.h $(INCDIR)

$(INCDIR)/Node.def.h: $(INCDIR)/Node.decl.h

$(INCDIR)/Node.decl.h: $(SRCDIR)/Node.ci
	$(CHARMXI) $(SRCDIR)/Node.ci
	$(MOVE) Node.def.h $(INCDIR)
	$(MOVE) Node.decl.h $(INCDIR)

$(INCDIR)/PatchMgr.def.h: $(INCDIR)/PatchMgr.decl.h

$(INCDIR)/PatchMgr.decl.h: $(SRCDIR)/PatchMgr.ci
	$(CHARMXI) $(SRCDIR)/PatchMgr.ci
	$(MOVE) PatchMgr.def.h $(INCDIR)
	$(MOVE) PatchMgr.decl.h $(INCDIR)

$(INCDIR)/ProxyMgr.def.h: $(INCDIR)/ProxyMgr.decl.h

$(INCDIR)/ProxyMgr.decl.h: $(SRCDIR)/ProxyMgr.ci
	$(CHARMXI) $(SRCDIR)/ProxyMgr.ci
	$(MOVE) ProxyMgr.def.h $(INCDIR)
	$(MOVE) ProxyMgr.decl.h $(INCDIR)

$(INCDIR)/ReductionMgr.def.h: $(INCDIR)/ReductionMgr.decl.h

$(INCDIR)/ReductionMgr.decl.h: $(SRCDIR)/ReductionMgr.ci
	$(CHARMXI) $(SRCDIR)/ReductionMgr.ci
	$(MOVE) ReductionMgr.def.h $(INCDIR)
	$(MOVE) ReductionMgr.decl.h $(INCDIR)

$(INCDIR)/Sync.def.h: $(INCDIR)/Sync.decl.h

$(INCDIR)/Sync.decl.h: $(SRCDIR)/Sync.ci
	$(CHARMXI) $(SRCDIR)/Sync.ci
	$(MOVE) Sync.def.h $(INCDIR)
	$(MOVE) Sync.decl.h $(INCDIR)

$(INCDIR)/WorkDistrib.def.h: $(INCDIR)/WorkDistrib.decl.h

$(INCDIR)/WorkDistrib.decl.h: $(SRCDIR)/WorkDistrib.ci
	$(CHARMXI) $(SRCDIR)/WorkDistrib.ci
	$(MOVE) WorkDistrib.def.h $(INCDIR)
	$(MOVE) WorkDistrib.decl.h $(INCDIR)

$(INCDIR)/main.def.h: $(INCDIR)/main.decl.h

$(INCDIR)/main.decl.h: $(SRCDIR)/main.ci
	$(CHARMXI) $(SRCDIR)/main.ci
	$(MOVE) main.def.h $(INCDIR)
	$(MOVE) main.decl.h $(INCDIR)

$(INCDIR)/AtomsDisInfo.def.h: $(INCDIR)/AtomsDisInfo.decl.h

$(INCDIR)/AtomsDisInfo.decl.h: $(SRCDIR)/AtomsDisInfo.ci
	$(CHARMXI) $(SRCDIR)/AtomsDisInfo.ci
	$(MOVE) AtomsDisInfo.def.h $(INCDIR)
	$(MOVE) AtomsDisInfo.decl.h $(INCDIR)

$(INCDIR)/FileIO.def.h: $(INCDIR)/FileIO.decl.h

$(INCDIR)/FileIO.decl.h: $(SRCDIR)/FileIO.ci
	$(CHARMXI) $(SRCDIR)/FileIO.ci
	$(MOVE) FileIO.def.h $(INCDIR)
	$(MOVE) FileIO.decl.h $(INCDIR)
@


1.1261
log
@Workaround to support both CUDA 2.2 and 2.3 (which adds lib64 directory)
without modifying arch/Linux-x86_64.cuda
@
text
@d176 2
d246 4
d350 1
a350 1
	-module NeighborLB -module commlib -language charm++ \
d593 14
@


1.1260
log
@update versions to 2.7b1 and charm-6.1.3
@
text
@d361 5
a365 1
	$(COPY) $(LIBCUDARTSODIR)/$(LIBCUDARTSO) $@@
@


1.1259
log
@Make that libcudart.so.2 and also copy it to build directory.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.7b1
@


1.1258
log
@include libcudart.so in release
@
text
@d338 1
a338 1
all:	$(BINARIES)
d359 3
@


1.1257
log
@Don't create .cubin file, use -Xptxas -v to get register information instead.
@
text
@d712 1
a712 1
RELEASE_FILES = flipdcd flipbinpdb psfgen charmrun namd2
@


1.1256
log
@Added ComputeNonbondedTabPot.[Ch]
@
text
@d279 1
a279 1
	$(CUDACC) $(COPTO)$(DSTDIR)/ComputeNonbondedCUDAKernel.o $(COPTC) $(SRCDIR)/ComputeNonbondedCUDAKernel.cu
a281 2
	$(CUDACC) -cubin $(SRCDIR)/ComputeNonbondedCUDAKernel.cu
	grep reg ComputeNonbondedCUDAKernel.cubin
@


1.1255
log
@New files added: 1. colvargrid.C,  2. colvargrid.h.  New features: 1) In the colvars components: added eigenvector.  Computes the projection of the coordinates on the NMA modes or some other vector field.  2) In metadynamics: can now change the size and resolution of the PMF grid.  Two options to do that are available:  a) by changing manually the grid's boundaries and width between one run and the other (keyword: rebinGrids), or  b) let the code itself expand the boundaries as needed (keyword: expandBoundaries).  3) In metadynamics: count the tails of those hills that lie close to the grid's edges; in some cases, this discontinuity, although right outside the PMF region, would previously result in some colvars getting stuck at the grid's edge in the long run.  4) Atom groups construction: define atoms by name that belong to different PSF segments (previously, only one PSF seg per group was allowed, otherwise atomNumbers was needed).  5) Colvars behaviour: define repulsive walls that don't coincide with the grid boundaries (make possible for the system to never leave the grid by any extent).  6) Cross time-correlation functions between two colvars (in addition to the ACFs).  7) Revised documentation: among several things, an example input file with actual keywords is shown instead of a *fake* one, and its syntax is now explained in more detail at the beginning.
@
text
@d109 1
@


1.1254
log
@Added ComputeGridForceMgr
@
text
@d158 1
@


1.1253
log
@Implement modified 1-4 exclusions for CUDA.
@
text
@d226 2
a361 1

d537 7
@


1.1252
log
@When making projections also enable summary because it's useful.
@
text
@d110 1
@


1.1251
log
@Fix winrelease target.
@
text
@d443 1
a443 1
	-tracemode projections \
@


1.1250
log
@Deal with compiler limitations by compiling second half of Molecule.C
as Molecule2.C.  Quick and dirty solution that can be refactored later.
@
text
@d357 4
a360 2
windowsbinaries: namd2.exe psfgen.exe
# windowsbinaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
d705 1
a705 1
WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmrun.exe charmd.exe charmd_faceless.exe $(TCLDLL)
d730 1
a730 1
	cp $(DOC_FILES) $(WIN32_RELEASE_FILES) $(RELEASE_DIR_NAME)
@


1.1249
log
@Update versions to NAMD 2.7b1 and Charm++ 6.1.
@
text
@d170 1
@


1.1248
log
@Switch Win32 to multicore.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.6
@


1.1247
log
@there is no reason to get summary logs with projections logs. It is annoying
when you do large processor runs.
@
text
@d356 2
a357 1
windowsbinaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
@


1.1246
log
@typo
@
text
@d421 1
a421 1
	-tracemode projections -tracemode summary \
d424 2
d432 1
a432 1
	-lm -o namd2
d439 1
a439 1
	-tracemode projections -tracemode summary \
d450 1
a450 1
	-lm -o namd2
d468 1
a468 1
	-lm -o namd2
@


1.1245
log
@Update psfgen to use plugins
@
text
@d386 1
a386 1
psfgen.exe:	$(DSTDIR) $(SBOBJS)  $(PLUGINOBJS)$(TCLDLL)
@


1.1244
log
@Cleanup Win32 build system.
@
text
@d295 1
d317 2
a318 2
SBCFLAGS = $(COPTI)$(SBSRCDIR) $(TCL) $(COPTS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
SBGCCFLAGS = $(COPTI)$(SBSRCDIR) $(TCL) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
d383 2
a384 2
psfgen:	$(DSTDIR) $(SBOBJS)
	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
d386 2
a387 2
psfgen.exe:	$(DSTDIR) $(SBOBJS) $(TCLDLL)
	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
@


1.1243
log
@Add --with-memopt option to config.
@
text
@a3 2
default: all

d12 3
d307 1
a307 1
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(COPTI)$(PLUGININCDIR) $(TCL) $(FFT) $(CUDA) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
d314 1
a314 1
PLUGINGCCFLAGS = $(COPTI)$(PLUGINSRCDIR) $(COPTI)$(PLUGININCDIR)
d357 1
a357 1
namd2.exe:  $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
d385 2
a386 2
psfgen.exe:	$(DSTDIR) $(SBOBJS)
	$(LINK) $(LINKOPTS) /out:psfgen.exe $(SBOBJS) $(TCLWINLIB) $(TCLAPPLIB)
@


1.1242
log
@New optimized pme header and source files.
@
text
@d41 2
a42 1
# to compile a memory optimized version, add -DMEM_OPT_VERSION
a44 1
#EXTRADEFINES=-DMEM_OPT_VERSION
d306 1
a306 1
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(COPTI)$(PLUGININCDIR) $(TCL) $(FFT) $(CUDA) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
@


1.1241
log
@Add rules for PluginIOMgr class
@
text
@d112 2
d225 4
d411 1
d507 7
d527 7
@


1.1240
log
@update dependencies for new plugins
@
text
@d205 1
@


1.1239
log
@CUDA support
@
text
@d252 4
a255 1
	$(DSTDIR)/dcdplugin.o
d627 1
a627 1
	      perl $(SRCDIR)/dc.pl $(PLUGINSRCDIR) $(PLUGININCDIR) /usr/include /usr/local >> $(DEPENDFILE); \
@


1.1238
log
@Added MGridforceParams.o
@
text
@d4 2
d52 2
d108 1
d256 12
d293 1
a293 1
LIBS = $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL)
d296 1
a296 1
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(COPTI)$(PLUGININCDIR) $(TCL) $(FFT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
d331 2
d352 2
d427 2
d445 2
@


1.1237
log
@Initial add of colvar module  (Following files added: src/GlobalMasterColvars.h src/colvar.C src/colvar.h src/colvaratoms.C src/colvaratoms.h src/colvarbias.C src/colvarbias.h src/colvarbias_abf.C src/colvarbias_abf.h src/colvarbias_meta.C src/colvarbias_meta.h src/colvarcomp.C src/colvarcomp.h src/colvarcomp_angles.C src/colvarcomp_coordnums.C src/colvarcomp_distances.C src/colvarcomp_protein.C src/colvarcomp_rotations.C src/colvarmodule.C src/colvarmodule.h src/colvarparse.C src/colvarparse.h src/colvarproxy.h src/colvarproxy_namd.C src/colvarproxy_namd.h src/colvartypes.h src/colvarvalue.C src/colvarvalue.h ug/ug_colvars.tex) --cbh
@
text
@d158 1
@


1.1236
log
@Fixed FileIO compile issues.
@
text
@d134 15
d200 2
a201 1
	$(DSTDIR)/FileIO.o
@


1.1235
log
@Added comment as how to compile a version that uses node aware proxy spanning tree.
@
text
@d184 2
a185 1
	$(DSTDIR)/AtomsDisInfo.o
d223 3
a225 1
		$(INCDIR)/AtomsDisInfo.def.h
d552 8
@


1.1234
log
@fix make clean to match new config script
@
text
@d40 1
d44 1
a44 1
EXTRADEFINES=-DREMOVE_PROXYRESULTMSG_EXTRACOPY
@


1.1233
log
@Smarted, more flexible config script.
@
text
@a607 2
	cd $(DPMTADIR) ; $(MAKE) clean ; cd ..
	cd $(DPMEDIR) ; $(MAKE) clean ; cd ..
@


1.1232
log
@Re-enable fixed extracopy parallel optimization.
@
text
@d10 1
a10 1
include Makearch
d50 1
a50 1
include Makearch
d425 1
a425 1
include Makearch
@


1.1231
log
@Disable buggy extracopy parallel optimization that was giving bad forces.
@
text
@d43 1
a43 1
#EXTRADEFINES=-DREMOVE_PROXYRESULTMSG_EXTRACOPY
@


1.1230
log
@Add flags for removing the extra copy overhead related to proxy msgs.
@
text
@d43 1
a43 1
EXTRADEFINES=-DREMOVE_PROXYRESULTMSG_EXTRACOPY
@


1.1229
log
@added targets for TorusLB and RefineTorusLB
@
text
@d39 5
a43 1
#MEMOPTDEF=-DMEM_OPT_VERSION
d258 1
a258 1
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(COPTI)$(PLUGININCDIR) $(TCL) $(FFT) $(CCS) $(RELEASE) $(MEMOPTDEF) $(TRACEOBJDEF)
d264 1
a264 1
CFLAGS = $(COPTI)$(SRCDIR) $(TCL) $(COPTS) $(RELEASE) $(MEMOPTDEF) $(TRACEOBJDEF)
d267 2
a268 2
SBCFLAGS = $(COPTI)$(SBSRCDIR) $(TCL) $(COPTS) $(RELEASE) $(MEMOPTDEF) $(TRACEOBJDEF)
SBGCCFLAGS = $(COPTI)$(SBSRCDIR) $(TCL) $(RELEASE) $(MEMOPTDEF) $(TRACEOBJDEF)
@


1.1228
log
@Updated Makefile and Make.depends for the addition of
GridForceGrid.[Ch]
@
text
@d164 1
d172 1
@


1.1227
log
@Changed the way to compile for tracing compute objects
@
text
@d129 1
@


1.1226
log
@Added compiling target for tracing compute objects
@
text
@d251 1
a251 1
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(COPTI)$(PLUGININCDIR) $(TCL) $(FFT) $(CCS) $(RELEASE) $(MEMOPTDEF)
d257 1
a257 1
CFLAGS = $(COPTI)$(SRCDIR) $(TCL) $(COPTS) $(RELEASE) $(MEMOPTDEF)
d260 2
a261 2
SBCFLAGS = $(COPTI)$(SBSRCDIR) $(TCL) $(COPTS) $(RELEASE) $(MEMOPTDEF)
SBGCCFLAGS = $(COPTI)$(SBSRCDIR) $(TCL) $(RELEASE) $(MEMOPTDEF)
d353 1
a353 1
#To compile tracecomputes, type the command "make tracecomputes CXXOPTS=-DTRACE_COMPUTE_OBJECTS $(CXXOPTS)"
@


1.1225
log
@Changes for two new files (AtomsDistInfo deals with using more charm arrays; CompressPsf deals with compressing a psf file)
@
text
@a38 1

d347 24
a370 1
projections:	$(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
d386 1
a386 1
summary:	$(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
@


1.1224
log
@Modifications for new feature, a Grid-based SMD feature, called Gridforce.
Gridforce applies forces to selected atoms from a DX potential file.
Coupling is electric charge.
This is the first version of this to appear in CVS.
@
text
@d39 3
d43 3
a45 3
CXXTHREADOPTS = $(CXXOPTS)
CXXSIMPARAMOPTS = $(CXXOPTS)
CXXNOALIASOPTS = $(CXXOPTS)
d175 3
a177 1
	$(DSTDIR)/imd.o
d213 3
a215 1
		$(INCDIR)/main.def.h
d252 1
a252 1
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(COPTI)$(PLUGININCDIR) $(TCL) $(FFT) $(CCS) $(RELEASE)
d258 1
a258 1
CFLAGS = $(COPTI)$(SRCDIR) $(TCL) $(COPTS) $(RELEASE)
d261 2
a262 2
SBCFLAGS = $(COPTI)$(SBSRCDIR) $(TCL) $(COPTS) $(RELEASE)
SBGCCFLAGS = $(COPTI)$(SBSRCDIR) $(TCL) $(RELEASE)
d512 7
@


1.1223
log
@Update to version 2.6.
@
text
@d87 1
@


1.1222
log
@Ignore errors from ldd (happens on XT3) on make release.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.6b2
@


1.1221
log
@Updates for 2.6b2 release.
@
text
@d596 1
a596 1
	for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done
@


1.1220
log
@Added support for "CMAP" crossterms from CHARMM31 forcefield.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.6b1
@


1.1219
log
@Justin's new pressure profile patch.
@
text
@d72 1
@


1.1218
log
@Justin's Targeted MD (TMD) patch.
@
text
@d78 1
d94 1
@


1.1217
log
@Run ldd separately on each binary.
@
text
@d52 1
d119 1
@


1.1216
log
@Run ldd (or otool -L on Mac) on binaries during "make release".
@
text
@d591 1
a591 1
	$(LDD) $(RELEASE_FILES)
@


1.1215
log
@Made changes for 64-bit windows
@
text
@d381 1
d569 1
a569 1
RELEASE_FILES = namd2 psfgen charmrun flipdcd flipbinpdb
d591 1
a591 2
	echo $(CHARM)
	file $(RELEASE_FILES)
@


1.1214
log
@Fix "make depends".
@
text
@d285 1
a285 1
win32binaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
@


1.1213
log
@Remove CVS directories from lib directory in release.
@
text
@d244 1
a244 1
GXXFLAGS = $(CXXBASEFLAGS)
@


1.1212
log
@Update version numbers to 2.6b1.
@
text
@d578 1
@


1.1211
log
@Add adaptive biasing force method from Chipot.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.5
@


1.1210
log
@List charm libraries when making release (saved by automated builds).
@
text
@d577 1
d596 1
@


1.1209
log
@Enable build info on Win32 (just assume they're using Cygwin)
@
text
@d586 3
d596 3
@


1.1208
log
@Include and build plugins with namd2 source, no longer separate library.
@
text
@d288 1
d291 1
@


1.1207
log
@Added tclBC --- Tcl boundary forces calculated per-atom
@
text
@d21 2
d206 5
d236 1
a236 1
LIBS = $(DPMTALIBS) $(DPMELIBS) $(TCLDLL)
d239 1
a239 1
CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(PLUGINS) $(TCL) $(FFT) $(CCS) $(RELEASE)
d246 2
d509 1
a509 1
	      perl $(SRCDIR)/dc.pl $(CHARMINC) $(TCLDIR) $(FFTDIR) $(PLUGINDIR) /usr/include /usr/local >> $(DEPENDFILE); \
d513 10
d527 1
a527 1
	      perl $(SRCDIR)/dc.pl $(CHARMINC) $(TCLDIR) $(FFTDIR) $(PLUGINDIR) /usr/include /usr/local >> $(DEPENDFILE); \
@


1.1206
log
@Tweaks for charm-5.8 and new platforms.
@
text
@d96 1
d500 1
a500 1
	      perl $(SRCDIR)/dc.pl $(CHARMINC) /usr/include /usr/local >> $(DEPENDFILE); \
d508 1
a508 1
	      perl $(SRCDIR)/dc.pl $(CHARMINC) /usr/include /usr/local >> $(DEPENDFILE); \
@


1.1205
log
@Sort objects, make depends.
@
text
@d269 1
d286 1
d336 1
d352 1
@


1.1204
log
@Bump version to 2.5.
@
text
@d67 2
d95 1
a95 2
	$(DSTDIR)/ComputeConsForce.o \
	$(DSTDIR)/ComputeConsForceMsgs.o \
a112 1
	$(DSTDIR)/ComputeStir.o \
@


1.1203
log
@Bump version to 2.5b3.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.5b3
@


1.1202
log
@Call it 2.5b2.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.5b2
@


1.1201
log
@pre3 -> pre4
@
text
@d2 1
a2 1
NAMD_VERSION = 2.5b2pre4
@


1.1200
log
@Changed version to 2.5b2pre3.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.5b2pre3
@


1.1199
log
@Added commlib to win32, projections, and summary builds.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.5b2pre2
@


1.1198
log
@2.5pre1 -> 2.5pre2
@
text
@d261 1
a261 1
	-module NeighborLB -language charm++ \
d269 1
a269 1
	-lm -o namd2 -module commlib
d278 1
a278 1
	-module NeighborLB -language charm++ \
d325 1
a325 1
	-module NeighborLB -language charm++ \
d340 2
a341 1
	-module NeighborLB -language charm++ -tracemode summary \
@


1.1197
log
@makefile changes for the communication library
@
text
@d2 1
a2 1
NAMD_VERSION = 2.5b2pre1
@


1.1196
log
@Version changed to 2.5b2pre1
@
text
@d269 1
a269 1
	-lm -o namd2
@


1.1195
log
@when compiling with trace projections, don't use tracemode all because trace projector is generating too many files.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.5b2ss03
@


1.1194
log
@Added CFLAGS to all CC lines.
@
text
@d325 2
a326 1
	-module NeighborLB -language charm++ -tracemode all \
@


1.1193
log
@Changed version to 2.5b2ss03 to indentify as summer school version.
@
text
@d303 1
a303 1
	$(CC) -o $@@ $(SRCDIR)/flipdcd.c || \
d308 1
a308 1
	$(CC) -o $@@ $(SRCDIR)/flipbinpdb.c || \
d313 1
a313 1
	$(CC) -o fixdcd $(SRCDIR)/fixdcd.c
d316 1
a316 1
	$(CC) -o dumpdcd $(SRCDIR)/dumpdcd.c
d319 1
a319 1
	$(CC) -o loaddcd $(SRCDIR)/loaddcd.c
@


1.1192
log
@Barry's torque application method.  "Stirring" atoms, constraining
only theta around a defined axis.
When used, writes to big auxlliary data file each time step step.
Still a little chatty; aux data file should be made more compact.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.5b2
@


1.1191
log
@Added "measure { consForceConfig <atomlist> <forcelist> }" command for
modifying constant forces on the fly.  Still undocumented (along with
all the other measure commands for that matter).  Also made errors in
the measure commands fatal; previously, any errors or error messages
were ignored.  The consForcefile parameter is now optional, since constant
forces can be specified at any time through the measure interface, though a
warning is issued if the filename is omitted.  Updated the docs a little
bit for the measure commands; still have lots to do here.
@
text
@d112 1
@


1.1190
log
@Split ComputeNonbondedBase.C into smaller files to build on T3E.
@
text
@d94 1
@


1.1189
log
@Added ComputeNonbondedBase.C to hold inner-loop and thus get rid of the
stupid Intel IA-64 compiler getting confused and not pipelining bug.
@
text
@d85 3
a87 1
	$(DSTDIR)/ComputeNonbondedBase.o \
d509 3
a511 1
	    -e "/obj\/ComputeNonbondedBase.o/ s/CXXFLAGS/CXXNOALIASFLAGS/" \
@


1.1188
log
@Added dumpbench tcl command to support NAMD serial benchmark.
@
text
@d85 1
d507 1
a507 1
	    -e "/obj\/ComputeNonbondedUtil.o/ s/CXXFLAGS/CXXNOALIASFLAGS/" \
@


1.1187
log
@Added build date/user/machine message on startup.
@
text
@d95 1
@


1.1186
log
@Version updates - now 2.5b2
@
text
@d239 10
d252 1
d256 1
d316 1
d320 1
d330 1
d334 1
@


1.1185
log
@Added CMK_OPTIMIZE=1 to all builds, which should eliminate verbose
"tracing not available" warnings.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.5b1
@


1.1184
log
@Added Settle, an analytical form of Shake/Rattle for waters.
@
text
@d218 1
a218 1
CHARMINC = $(CHARM)/include
d225 6
a230 5
CXXFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(PLUGINS) $(TCL) $(FFT) $(CCS) $(CXXOPTS) $(RELEASE) $(NEWMASTER) $(NEWMASTER)
CXXTHREADFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(PLUGINS) $(TCL) $(FFT) $(CCS) $(CXXTHREADOPTS) $(RELEASE)
CXXSIMPARAMFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXSIMPARAMOPTS) $(RELEASE) $(NEWMASTER)
CXXNOALIASFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXNOALIASOPTS) $(RELEASE) $(NEWMASTER)
GXXFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(RELEASE) $(NEWMASTER)
@


1.1183
log
@Added PLUGINLIB to all targets.
@
text
@d149 1
@


1.1182
log
@Added support for building with plugins.
@
text
@d264 1
d305 1
a305 1
	-o namd2 $(OBJS) \
d309 3
a311 1
	$(FFTLIB)
d317 1
a317 1
	-o namd2 $(OBJS) \
d321 3
a323 1
	$(FFTLIB)
@


1.1181
log
@Added file command to release target, to check for dynamic executables.
@
text
@a21 1
PLUGINDIR = plugins
a35 6

# comment/uncomment for file I/O plugins
#PLUGININCL=$(COPTI)$(PLUGINDIR)
#PLUGINLIB=-L$(PLUGINDIR) -lmolfile_plugin
#PLUGINFLAGS=$(COPTD)NAMD_PLUGINS
#PLUGINS=$(PLUGININCL) $(PLUGINFLAGS)
@


1.1180
log
@now use +tracemode all to generate both projections and summary logs, this is now becoming the standard way of generating log files for projections tool.
@
text
@d534 1
@


1.1179
log
@Added a PLUGINS option to the Makefile.  Implemented a Tcl command "coorfile"
which reads trajectory files and resets NAMD's coordinates from the
timesteps.  The implementation could be improved but the Tcl interface is
flexible enough to support multiple coordinate file types.
@
text
@d310 1
a310 1
	-module NeighborLB -language charm++ -tracemode projections \
@


1.1178
log
@Updated version to 2.5b1.
@
text
@d22 1
d38 6
d231 2
a232 2
CXXFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXOPTS) $(RELEASE) $(NEWMASTER) $(NEWMASTER)
CXXTHREADFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXTHREADOPTS) $(RELEASE)
d255 1
@


1.1177
log
@Updated version to 2.4.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.4
@


1.1176
log
@Small Windows/Tcl hack.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.4b2
@


1.1175
log
@Using conventional charm link method.
@
text
@d278 1
a278 1
	$(LINK) $(LINKOPTS) /out:psfgen.exe $(SBOBJS) $(TCLLIB) $(TCLAPPLIB)
@


1.1174
log
@Fixed on win32 to use charmc to generate moduleinit.[Co].
@
text
@d255 3
a257 4
namd2.exe:  $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) $(DSTDIR)/moduleinit.o
	$(LINK) $(LINKOPTS) /nodefaultlib:libc /nodefaultlib:libcmt.lib \
	/out:namd2.exe \
	$(CHARMLIB)/libldb-rand.o \
a258 7
	$(DSTDIR)/moduleinit.o \
	$(CHARMLIB)/libmoduleNeighborLB.a \
	$(CHARMLIB)/libck.a \
	$(CHARMLIB)/libconv-cplus-y.a \
	$(CHARMLIB)/libconv-core.a \
	$(CHARMLIB)/libconv-util.a \
	$(CHARMLIB)/libmemory-default.o \
d262 2
a263 5
	$(FFTLIB)

$(DSTDIR)/moduleinit.o:
	-cd $(DSTDIR); \
	$(CHARMC) -module NeighborLB -language charm++ fail.o -o fail
@


1.1173
log
@Removed libtrace-none.a from win32 explicit link list.
@
text
@d259 5
a264 2
	$(CHARMLIB)/libconv-cplus-y.a \
	$(CHARMLIB)/libck.a \
a266 2
	$(CHARMLIB)/libmoduleNeighborLB.a \
	$(OBJS) $(DSTDIR)/moduleinit.o \
d272 3
a274 2
$(DSTDIR)/moduleinit.o: src/moduleinit.C
	$(CXX) $(CXXFLAGS) $(COPTO)obj/moduleinit.o $(COPTC) src/moduleinit.C
@


1.1172
log
@Updated version to 2.4b2.
@
text
@a258 1
	$(CHARMLIB)/libtrace-none.a \
@


1.1171
log
@Moved psfgen to separate directory tree based on Justin's version.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.4b1
@


1.1170
log
@Changes for version 2.4b1.
@
text
@d21 1
d197 2
a198 1
	$(DSTDIR)/build.o \
d230 2
d285 1
a285 1
	$(CC) $(CFLAGS) -o psfgen $(SBOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
d478 1
a478 1
	      SRCFILE=$(SRCDIR)/`basename $$i .o`.c ; \
d480 1
a480 1
	      gcc -MM $(GCCFLAGS) $$SRCFILE | \
d482 1
a482 1
	      $(ECHO) '	$$(CC) $$(CFLAGS) $$(COPTO)'$$i '$$(COPTC)' \
@


1.1169
log
@Changed version to 2.4a1.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.4a1
@


1.1168
log
@forgot -module for make projections and summey.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.3
@


1.1167
log
@this is for win32 version with new load balancer module.
@
text
@d308 1
a308 1
	-language charm++ -tracemode projections \
d318 1
a318 1
	-language charm++ -tracemode summary \
@


1.1166
log
@added -module NeighborLB because charm++ load balancer now becomes a module.
@
text
@d251 3
a253 2
namd2.exe:  $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
	$(LINK) $(LINKOPTS) /nodefaultlib:libc /out:namd2.exe \
d261 2
a262 1
	$(OBJS) \
d267 3
@


1.1165
log
@Adding support for multiple masters.  You can now run IMD at the
same time as Tcl at the same time as SMD, etc.  Lots of things
have been renamed to make this happen!
@
text
@d238 1
a238 1
	-language charm++ \
@


1.1164
log
@Added Sync... to CIFILES list.
@
text
@a72 1
	$(DSTDIR)/ComputeFreeEnergy.o \
a77 2
	$(DSTDIR)/ComputeGlobalEasy.o \
	$(DSTDIR)/ComputeGlobalMaster.o \
a78 1
	$(DSTDIR)/ComputeIMD.o \
a79 1
	$(DSTDIR)/ComputeMisc.o \
a87 1
	$(DSTDIR)/ComputeSMD.o \
a88 1
	$(DSTDIR)/ComputeTcl.o \
d102 9
d222 1
a222 1
CXXFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXOPTS) $(RELEASE)
d224 3
a226 3
CXXSIMPARAMFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXSIMPARAMOPTS) $(RELEASE)
CXXNOALIASFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXNOALIASOPTS) $(RELEASE)
GXXFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(RELEASE)
d246 1
a246 1
charmrun:
@


1.1163
log
@Added ComputeExt... (forces calculated by external command).
@
text
@d184 2
@


1.1162
log
@updated Makefile for Neighbor lbdb.
@
text
@d72 1
d168 2
d369 7
@


1.1161
log
@Added GromacsTopFile to the makefile.
@
text
@d55 1
d120 1
d171 2
d380 7
@


1.1160
log
@Added CXXNOALIASOPTS for ComputeNonbondedUtil.o compilation.
@
text
@d107 1
@


1.1159
log
@Win32 version need to specify libmemory-default.o of Charm++.
@
text
@d39 1
d213 1
d456 1
@


1.1158
log
@Updated version to 2.3.
@
text
@d245 1
@


1.1157
log
@Added DataStream.C for auxiliary data stream output.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.3b2
@


1.1156
log
@Add file ComputeConsForce.o for constant force feature.
@
text
@d97 1
@


1.1155
log
@Added parm.[Ch].
@
text
@d93 1
@


1.1154
log
@eliminating redundancies in .arch files
@
text
@d145 1
@


1.1153
log
@version 2.3b2
@
text
@d13 1
a13 1
RELEASE=$(COPTD)NAMD_VERSION=\"$(NAMD_VERSION)\" $(COPTD)NAMD_PLATFORM=\"$(NAMD_PLATFORM)\"
d35 4
@


1.1152
log
@Changes to use cygwin make rather than nmake on Win32.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.3b1
@


1.1151
log
@Added psf_file and psf_file_extract.
@
text
@d245 1
a245 1
	$(COPY) $(CHARM)\bin\charmd.exe charmd.exe
d248 1
a248 1
	$(COPY) $(CHARM)\bin\charmd_faceless.exe charmd_faceless.exe
d251 1
a251 1
	$(COPY) $(CHARM)\bin\charmrun.exe charmrun.exe
@


1.1150
log
@for namd2.exe under NT, changed obj/*.o for namd2.exe action in Makefile to  $(OBJS), because re-compilation will include *.o from psfgen and duplicate main in mainfunc and build.o.
@
text
@d185 2
@


1.1149
log
@add load balancing strategy "rob" as in SimParameters, which is a recursion of bisection algorithm to partition the computes.
@
text
@d236 1
a236 1
	obj/*.o \
@


1.1148
log
@Added external electric field.
@
text
@d49 1
@


1.1147
log
@Version 2.3b1
@
text
@d64 1
@


1.1146
log
@Convert text files to DOS format.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.3a3
@


1.1145
log
@Fixes to build on Win32 under Cygwin.
@
text
@d466 1
a466 4
DOC_FILES = .rootdir/README.txt \
	.rootdir/announce.txt \
	.rootdir/license.txt \
	.rootdir/notes.txt
d468 1
a468 1
RELEASE_FILES = $(DOC_FILES) namd2 psfgen charmrun flipdcd flipbinpdb
d470 1
a470 1
WIN32_RELEASE_FILES = $(DOC_FILES) namd2.exe psfgen.exe charmrun.exe charmd.exe charmd_faceless.exe $(TCLDLL)
d476 1
d490 1
a490 1
	cp $(WIN32_RELEASE_FILES) $(RELEASE_DIR_NAME)
@


1.1144
log
@Version 2.3a3.
@
text
@d227 7
a233 7
	$(LINK) $(LINKOPTS) /out:namd2.exe \
	$(CHARMLIB)/libldb-rand.obj \
	$(CHARMLIB)/libtrace-none.lib \
	$(CHARMLIB)/libconv-core.lib \
	$(CHARMLIB)/libconv-cplus-y.lib \
	$(CHARMLIB)/libck.lib \
	$(CHARMLIB)/libutil.lib \
@


1.1143
log
@Added TCLAPPLIB make var.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.3a2
@


1.1142
log
@Added Tcl to psfgen.
@
text
@d250 1
a250 1
	$(CC) $(CFLAGS) -o psfgen $(SBOBJS) $(TCLLIB) -lsocket -lnsl -lm
d253 1
a253 1
	$(LINK) $(LINKOPTS) /out:psfgen.exe $(SBOBJS) $(TCLLIB)
@


1.1141
log
@Switched conv-host to charmrun, added charmd to release.
@
text
@d250 1
a250 1
	$(CC) $(CFLAGS) -o psfgen $(SBOBJS) -lm
d253 1
a253 1
	$(LINK) $(LINKOPTS) /out:psfgen.exe $(SBOBJS)
@


1.1140
log
@Eliminated awk, now just uses basename in make depends.
@
text
@d206 1
a206 1
BINARIES = namd2 psfgen flipdcd flipbinpdb
d214 1
a214 1
	-o namd2 $(OBJS) \
d218 5
a222 1
	$(FFTLIB)
d224 1
a224 1
win32binaries: namd2.exe psfgen.exe daemon.exe daemon_background.exe conv-host.exe
d240 2
a241 2
daemon.exe:
	$(COPY) $(CHARM)\bin\daemon.exe daemon.exe
d243 2
a244 2
daemon_background.exe:
	$(COPY) $(CHARM)\bin\daemon_background.exe daemon_background.exe
d246 2
a247 2
conv-host.exe:
	$(COPY) $(CHARM)\bin\conv-host.exe conv-host.exe
d471 1
a471 1
RELEASE_FILES = $(DOC_FILES) namd2 flipdcd flipbinpdb
d473 1
a473 1
WIN32_RELEASE_FILES = $(DOC_FILES) namd2.exe conv-host.exe daemon.exe daemon_background.exe $(TCLDLL)
d479 5
a483 4
	if [ -r conv-host ]; then \
	   $(COPY) conv-host $(RELEASE_DIR_NAME); \
	   $(ECHO) "group main" > $(RELEASE_DIR_NAME)/nodelist; \
	   $(ECHO) " host localhost" >> $(RELEASE_DIR_NAME)/nodelist; \
a492 2
	$(ECHO) "group main" > $(RELEASE_DIR_NAME)/nodelist; \
	$(ECHO) " host localhost" >> $(RELEASE_DIR_NAME)/nodelist; \
@


1.1139
log
@Adding structure building code to CVS.
@
text
@a408 2
# make depends is ugly!  The problem: we have obj/file.o and want src/file.C.
# Solution: heavy use of basename and awk.
d417 1
a417 1
	      SRCFILE=$(SRCDIR)/`basename $$i | awk -F. '{print $$1".C"}'` ; \
d425 1
a425 1
	      SRCFILE=$(SRCDIR)/`basename $$i | awk -F. '{print $$1".c"}'` ; \
@


1.1138
log
@Version 2.3a2
@
text
@d171 17
d202 1
d206 1
a206 1
BINARIES = namd2 flipdcd flipbinpdb
d220 1
a220 1
win32binaries: namd2.exe daemon.exe daemon_background.exe conv-host.exe
d245 6
d419 3
a421 4
	      $(ECHO) "checking dependencies for" \
	        `basename $$i | awk -F. '{print $$1".C"}'` ; \
	      g++ -MM $(GXXFLAGS) \
	        $(SRCDIR)/`basename $$i | awk -F. '{print $$1".C"}'` | \
d424 9
a432 2
	        $(SRCDIR)/`basename $$i | awk -F. '{print $$1".C"}'` \
		>> $(DEPENDFILE) ; \
@


1.1137
log
@Version 2.3a1.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.3a1
@


1.1136
log
@Turned off default compile of DPMTA and DPME.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.2
@


1.1135
log
@Updated to 2.2, added release notes.
@
text
@d23 5
a27 5
DPMTAINCL=$(COPTI)$(DPMTADIR)/mpole $(COPTI)$(DPMTADIR)/src
DPMTALIB=-L$(DPMTADIR)/mpole -L$(DPMTADIR)/src -ldpmta2 -lmpole -lpvmc
DPMTAFLAGS=$(COPTD)DPMTA
DPMTA=$(DPMTAINCL) $(DPMTAFLAGS)
DPMTALIBS=$(DPMTADIR)/mpole/libmpole.a $(DPMTADIR)/src/libdpmta2.a
d30 5
a34 5
DPMEINCL=$(COPTI)$(DPMEDIR)
DPMELIB=-L$(DPMEDIR) -ldpme
DPMEFLAGS=$(COPTD)DPME
DPME=$(DPMEINCL) $(DPMEFLAGS)
DPMELIBS= $(DPMEDIR)/libdpme.a
@


1.1134
log
@Added daemon_background.exe to windows archive.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.2b3
@


1.1133
log
@Updated version to 2.2b3.
@
text
@d441 1
a441 1
WIN32_RELEASE_FILES = $(DOC_FILES) namd2.exe conv-host.exe daemon.exe $(TCLDLL)
@


1.1132
log
@Fixes to work with the new version of Charm.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.2b2
@


1.1131
log
@Turned on and fixed erf() and erfc() for Win32.
@
text
@d202 1
a202 1
win32binaries: namd2.exe daemon.exe conv-host.exe
d211 1
d220 3
@


1.1130
log
@Added winrelease target to build zip files.
@
text
@d43 1
@


1.1129
log
@Reversed order of moves for .def and .decl files.
@
text
@d216 1
a216 1
daemon.exe:  $(CHARM)\bin\daemon.exe
d219 1
a219 1
conv-host.exe:  $(CHARM)\bin\conv-host.exe
d428 9
a436 5
RELEASE_FILES = .rootdir/README.txt \
		.rootdir/announce.txt \
		.rootdir/license.txt \
		.rootdir/notes.txt \
		namd2 flipdcd flipbinpdb
d450 9
@


1.1128
log
@Tcl and FFTW now work on Win32.
@
text
@d284 1
a285 1
	$(MOVE) BroadcastMgr.def.h $(INCDIR)
d291 1
a292 1
	$(MOVE) CollectionMaster.def.h $(INCDIR)
d298 1
a299 1
	$(MOVE) CollectionMgr.def.h $(INCDIR)
d305 1
a306 1
	$(MOVE) ComputeMgr.def.h $(INCDIR)
d312 1
a313 1
	$(MOVE) ComputePmeMgr.def.h $(INCDIR)
d319 1
a320 1
	$(MOVE) LdbCoordinator.def.h $(INCDIR)
d326 1
a327 1
	$(MOVE) NamdCentLB.def.h $(INCDIR)
d333 1
a334 1
	$(MOVE) Node.def.h $(INCDIR)
d340 1
a341 1
	$(MOVE) PatchMgr.def.h $(INCDIR)
d347 1
a348 1
	$(MOVE) ProxyMgr.def.h $(INCDIR)
d354 1
a355 1
	$(MOVE) ReductionMgr.def.h $(INCDIR)
d361 1
a362 1
	$(MOVE) Sync.def.h $(INCDIR)
d368 1
a369 1
	$(MOVE) WorkDistrib.def.h $(INCDIR)
d375 1
a376 1
	$(MOVE) main.def.h $(INCDIR)
@


1.1127
log
@Updated version to 2.2b2.
@
text
@d177 1
a177 1
LIBS = $(DPMTALIBS) $(DPMELIBS)
@


1.1126
log
@Added LINKOPTS for Win32.
@
text
@d2 1
a2 1
NAMD_VERSION = 2.2b1
@


1.1125
log
@One Makefile now builds Win32 and unix.
@
text
@d204 1
a204 1
	$(LINK) /out:namd2.exe \
@


1.1124
log
@Only one file per MOVE for Windows.
@
text
@d1 9
d13 1
a13 2
NAMD_VERSION = 2.2b1
RELEASE=-DNAMD_VERSION=\"$(NAMD_VERSION)\" -DNAMD_PLATFORM=\"$(NAMD_PLATFORM)\"
d23 1
a23 1
DPMTAINCL=-I$(DPMTADIR)/mpole -I$(DPMTADIR)/src
d25 1
a25 1
DPMTAFLAGS=-DDPMTA
d30 1
a30 1
DPMEINCL=-I$(DPMEDIR)
d32 1
a32 1
DPMEFLAGS=-DDPME
d36 2
d173 2
a174 1
INCLUDE = $(CHARM)/include
d180 4
a183 4
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXOPTS) $(RELEASE)
CXXTHREADFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXTHREADOPTS) $(RELEASE)
CXXSIMPARAMFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXSIMPARAMOPTS) $(RELEASE)
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(RELEASE)
d193 1
a193 1
	"-I$(INCLUDE) -I$(INCDIR) -I$(SRCDIR) $(CXXOPTS)" \
d201 21
d243 1
a243 1
	"-I$(INCLUDE) -I$(INCDIR) -I$(SRCDIR) $(CXXOPTS)" \
d253 1
a253 1
	"-I$(INCLUDE) -I$(INCDIR) -I$(SRCDIR) $(CXXOPTS)" \
d276 2
d394 2
a395 2
	      perl $(SRCDIR)/dc.pl $(INCLUDE) /usr/include /usr/local >> $(DEPENDFILE); \
	      $(ECHO) '	$$(CXX) $$(CXXFLAGS)' -o $$i -c \
d411 1
a411 1
include	$(DEPENDFILE)
@


1.1123
log
@Declaring official 2.2b1.
@
text
@d250 2
a251 1
	$(MOVE) BroadcastMgr.decl.h BroadcastMgr.def.h $(INCDIR)
d257 2
a258 1
	$(MOVE) CollectionMaster.decl.h CollectionMaster.def.h $(INCDIR)
d264 2
a265 1
	$(MOVE) CollectionMgr.decl.h CollectionMgr.def.h $(INCDIR)
d271 2
a272 1
	$(MOVE) ComputeMgr.decl.h ComputeMgr.def.h $(INCDIR)
d278 2
a279 1
	$(MOVE) ComputePmeMgr.decl.h ComputePmeMgr.def.h $(INCDIR)
d285 2
a286 1
	$(MOVE) LdbCoordinator.decl.h LdbCoordinator.def.h $(INCDIR)
d292 2
a293 1
	$(MOVE) NamdCentLB.decl.h NamdCentLB.def.h $(INCDIR)
d299 2
a300 1
	$(MOVE) Node.decl.h Node.def.h $(INCDIR)
d306 2
a307 1
	$(MOVE) PatchMgr.decl.h PatchMgr.def.h $(INCDIR)
d313 2
a314 1
	$(MOVE) ProxyMgr.decl.h ProxyMgr.def.h $(INCDIR)
d320 2
a321 1
	$(MOVE) ReductionMgr.decl.h ReductionMgr.def.h $(INCDIR)
d327 2
a328 1
	$(MOVE) Sync.decl.h Sync.def.h $(INCDIR)
d334 2
a335 1
	$(MOVE) WorkDistrib.decl.h WorkDistrib.def.h $(INCDIR)
d341 2
a342 1
	$(MOVE) main.decl.h main.def.h $(INCDIR)
@


1.1122
log
@Added memory usage tracking.
@
text
@d4 1
a4 1
NAMD_VERSION = 2.1
@


1.1121
log
@Removed fftw directory.
@
text
@d35 1
@


1.1120
log
@Removed old/unused exclusion checking code.
@
text
@d168 4
a171 4
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) -Ifftw $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXOPTS) $(RELEASE)
CXXTHREADFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) -Ifftw $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXTHREADOPTS) $(RELEASE)
CXXSIMPARAMFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) -Ifftw $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXSIMPARAMOPTS) $(RELEASE)
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) -Ifftw $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(RELEASE)
a373 1
	cd fftw ; $(MAKE) clean ; cd ..
@


1.1119
log
@Removing old/unused PME code.
@
text
@a64 1
	$(DSTDIR)/ComputeNonbondedExcl.o \
@


1.1118
log
@Removing old/unused PME code.
@
text
@a109 2
	$(DSTDIR)/PmeCoulomb.o \
	$(DSTDIR)/PmeFFT.o \
d166 1
a166 1
LIBS = $(DPMTALIBS) $(DPMELIBS) fftw/libfftw_ampi.a
d183 1
a183 1
	-language ampi \
a186 1
	-Lfftw -lfftw_ampi \
d212 1
a212 1
	-language ampi -tracemode projections \
a215 1
	-Lfftw -lfftw_ampi \
d222 1
a222 1
	-language ampi -tracemode summary \
a225 1
	-Lfftw -lfftw_ampi \
a235 3

fftw/libfftw_ampi.a:
	cd fftw ; $(MAKE) ; cd ..
@


1.1117
log
@Fixed race condition when using gmake.
@
text
@a71 1
	$(DSTDIR)/ComputePmeMsgs.o \
@


1.1116
log
@Builds without FFTW again.
@
text
@d235 1
a235 2
$(DPMTADIR)/mpole/libmpole.a:
	cd $(DPMTADIR) ; $(MAKE) ; cd ..
@


1.1115
log
@Parallel PME reciprocal sum.
@
text
@d172 4
a175 4
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXOPTS) $(RELEASE)
CXXTHREADFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXTHREADOPTS) $(RELEASE)
CXXSIMPARAMFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXSIMPARAMOPTS) $(RELEASE)
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(RELEASE)
d190 1
d220 1
d231 1
@


1.1114
log
@Incorporated AMPI version of FFTW.
@
text
@d144 2
d186 1
a186 1
	-language charm++ \
d215 1
a215 1
	-language charm++ -tracemode projections \
d225 1
a225 1
	-language charm++ -tracemode summary \
d276 6
@


1.1113
log
@Changes to build Sync.
@
text
@d167 1
a167 1
LIBS = $(DPMTALIBS) $(DPMELIBS)
d239 3
d374 1
@


1.1112
log
@Makearch now includes Make.charm.
@
text
@d126 1
d307 6
@


1.1111
log
@Now using pvm lib in charm source.
@
text
@a0 1
include .rootdir/Make.charm
@


1.1110
log
@Cleanup load balance changes.
@
text
@a12 1
PVMDIR=pvm3
d16 2
a17 2
DPMTAINCL=-I$(DPMTADIR)/mpole -I$(DPMTADIR)/src -I$(PVMDIR)
DPMTALIB=-L$(DPMTADIR)/mpole -L$(DPMTADIR)/src -ldpmta2 -lmpole -L$(PVMDIR) -lpvmc
d20 1
a20 1
DPMTALIBS=$(DPMTADIR)/mpole/libmpole.a $(DPMTADIR)/src/libdpmta2.a $(PVMDIR)/libpvmc.a
a238 3
$(PVMDIR)/libpvmc.a:
	cd $(PVMDIR) ; $(MAKE) ; cd ..

a363 1
	cd $(PVMDIR) ; $(MAKE) clean ; cd ..
@


1.1109
log
@Added NamdCentLB.C, which uses new load balancing framework inside of
charm++
@
text
@d278 1
a278 2
$(INCDIR)/LdbCoordinator.decl.h: $(SRCDIR)/LdbCoordinator.ci \
	$(INCDIR)/NamdCentLB.decl.h
@


1.1108
log
@Added usage tracking code.
@
text
@d100 1
d147 2
d278 2
a279 1
$(INCDIR)/LdbCoordinator.decl.h: $(SRCDIR)/LdbCoordinator.ci
d282 6
@


1.1107
log
@Major cleanup.
@
text
@d4 4
d168 4
a171 4
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXOPTS)
CXXTHREADFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXTHREADOPTS)
CXXSIMPARAMFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS) $(CXXSIMPARAMOPTS)
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CCS)
a364 1
NAMD_VERSION = 2.1
@


1.1106
log
@Added ability to write "measurements" for Tcl scripts.
@
text
@a87 1
	$(DSTDIR)/HBondParam.o \
a88 1
	$(DSTDIR)/Inform.o \
a123 1
	$(DSTDIR)/VoidTree.o \
@


1.1105
log
@Fixed spelling error.
@
text
@d94 1
@


1.1104
log
@Removed long-broken TestSequencer and TestController.
@
text
@d189 1
a189 1
	echo "#!/bin/sh\necho unavailable on this platfrom" > $@@; \
d194 1
a194 1
	echo "#!/bin/sh\necho unavailable on this platfrom" > $@@; \
@


1.1103
log
@Rearranging for frontend/backend separation.
@
text
@a124 2
	$(DSTDIR)/TestController.o \
	$(DSTDIR)/TestSequencer.o \
a336 2
	    -e "/obj\/TestController.o/ s/CXXFLAGS/CXXTHREADFLAGS/" \
	    -e "/obj\/TestSequencer.o/ s/CXXFLAGS/CXXTHREADFLAGS/" \
@


1.1102
log
@Fixes permissions before tar on Make release.
@
text
@a96 1
	$(DSTDIR)/Namd.o \
@


1.1101
log
@Moving code around for API.
@
text
@d385 1
@


1.1100
log
@Purged dead code.
@
text
@d36 1
@


1.1099
log
@Added tracemode summary compilation
@
text
@a53 1
	$(DSTDIR)/ComputeGeneral.o \
@


1.1098
log
@Refactoring startup/control for frontend separation.
@
text
@d219 10
@


1.1097
log
@Removed SMD.* and SMDMsgs.*.  Refactored ComputeSMD as a ComputeGlobalMaster and
updated dependencies.
@
text
@d32 1
a77 1
        $(DSTDIR)/defmain.o \
@


1.1096
log
@Updated version to 2.1.
@
text
@a124 2
	$(DSTDIR)/SMD.o \
	$(DSTDIR)/SMDMsgs.o \
@


1.1095
log
@Creates dummy executables if flipdcd and flipbinpdb don't compile (T3E).
@
text
@d360 1
a360 1
NAMD_VERSION = 2.1b4
@


1.1094
log
@Cleaned up .ci/.decl.h/.def.h dependencies for gmake -j parallel make.
@
text
@d193 3
a195 1
	$(CC) -o flipdcd $(SRCDIR)/flipdcd.c
d198 3
a200 1
	$(CC) -o flipbinpdb $(SRCDIR)/flipbinpdb.c
@


1.1093
log
@Fixed "make release" for Solaris.
@
text
@d238 1
a238 1
MOVECIFILES = $(MOVE) *.decl.h *.def.h $(INCDIR)
d240 1
a240 1
$(INCDIR)/BroadcastMgr.decl.h:	$(SRCDIR)/BroadcastMgr.ci
d242 1
a242 1
	$(MOVECIFILES)
d244 1
a244 7
$(INCDIR)/BroadcastMgr.def.h:	$(SRCDIR)/BroadcastMgr.ci
	$(CHARMXI) $(SRCDIR)/BroadcastMgr.ci
	$(MOVECIFILES)

$(INCDIR)/CollectionMaster.decl.h:	$(SRCDIR)/CollectionMaster.ci
	$(CHARMXI) $(SRCDIR)/CollectionMaster.ci
	$(MOVECIFILES)
d246 1
a246 1
$(INCDIR)/CollectionMaster.def.h:	$(SRCDIR)/CollectionMaster.ci
d248 1
a248 1
	$(MOVECIFILES)
d250 1
a250 3
$(INCDIR)/CollectionMgr.decl.h:	$(SRCDIR)/CollectionMgr.ci
	$(CHARMXI) $(SRCDIR)/CollectionMgr.ci
	$(MOVECIFILES)
d252 1
a252 1
$(INCDIR)/CollectionMgr.def.h:	$(SRCDIR)/CollectionMgr.ci
d254 1
a254 1
	$(MOVECIFILES)
d256 1
a256 3
$(INCDIR)/ComputeMgr.decl.h:	$(SRCDIR)/ComputeMgr.ci
	$(CHARMXI) $(SRCDIR)/ComputeMgr.ci
	$(MOVECIFILES)
d258 1
a258 1
$(INCDIR)/ComputeMgr.def.h:	$(SRCDIR)/ComputeMgr.ci
d260 1
a260 1
	$(MOVECIFILES)
d262 1
a262 3
$(INCDIR)/LdbCoordinator.decl.h:	$(SRCDIR)/LdbCoordinator.ci
	$(CHARMXI) $(SRCDIR)/LdbCoordinator.ci
	$(MOVECIFILES)
d264 1
a264 1
$(INCDIR)/LdbCoordinator.def.h:	$(SRCDIR)/LdbCoordinator.ci
d266 1
a266 1
	$(MOVECIFILES)
d268 1
a268 3
$(INCDIR)/Node.decl.h:	$(SRCDIR)/Node.ci
	$(CHARMXI) $(SRCDIR)/Node.ci
	$(MOVECIFILES)
d270 1
a270 1
$(INCDIR)/Node.def.h:	$(SRCDIR)/Node.ci
d272 1
a272 1
	$(MOVECIFILES)
d274 1
a274 3
$(INCDIR)/PatchMgr.decl.h:	$(SRCDIR)/PatchMgr.ci
	$(CHARMXI) $(SRCDIR)/PatchMgr.ci
	$(MOVECIFILES)
d276 1
a276 1
$(INCDIR)/PatchMgr.def.h:	$(SRCDIR)/PatchMgr.ci
d278 1
a278 1
	$(MOVECIFILES)
d280 1
a280 3
$(INCDIR)/ProxyMgr.decl.h:	$(SRCDIR)/ProxyMgr.ci
	$(CHARMXI) $(SRCDIR)/ProxyMgr.ci
	$(MOVECIFILES)
d282 1
a282 1
$(INCDIR)/ProxyMgr.def.h:	$(SRCDIR)/ProxyMgr.ci
d284 1
a284 1
	$(MOVECIFILES)
d286 1
a286 3
$(INCDIR)/ReductionMgr.decl.h:	$(SRCDIR)/ReductionMgr.ci
	$(CHARMXI) $(SRCDIR)/ReductionMgr.ci
	$(MOVECIFILES)
d288 1
a288 1
$(INCDIR)/ReductionMgr.def.h:	$(SRCDIR)/ReductionMgr.ci
d290 1
a290 1
	$(MOVECIFILES)
d292 1
a292 3
$(INCDIR)/WorkDistrib.decl.h:	$(SRCDIR)/WorkDistrib.ci
	$(CHARMXI) $(SRCDIR)/WorkDistrib.ci
	$(MOVECIFILES)
d294 1
a294 1
$(INCDIR)/WorkDistrib.def.h:	$(SRCDIR)/WorkDistrib.ci
d296 1
a296 1
	$(MOVECIFILES)
d298 1
a298 3
$(INCDIR)/main.decl.h:	$(SRCDIR)/main.ci
	$(CHARMXI) $(SRCDIR)/main.ci
	$(MOVECIFILES)
d300 1
a300 1
$(INCDIR)/main.def.h:	$(SRCDIR)/main.ci
d302 1
a302 1
	$(MOVECIFILES)
@


1.1092
log
@Updated version number to 2.1b4.
@
text
@d392 1
a392 1
	if [ -e conv-host ]; then \
@


1.1091
log
@Revamped config and make system.
@
text
@d380 1
a380 1
NAMD_VERSION = 2.1b3
@


1.1090
log
@Added ability to "make release".
@
text
@d1 1
a1 1
include Make.charm
d328 1
a328 1
DEPENDFILE = Make.depends
d381 1
a381 1
RELEASE_DIR_NAME = NAMD_$(NAMD_VERSION)_$(NAMD_ARCH)
@


1.1089
log
@Separated ComputeHomePatch from ComputePatch.
@
text
@d380 20
@


1.1088
log
@Cleaned up CCS compilation.
@
text
@d50 1
@


1.1087
log
@Removed dead files.
@
text
@d170 4
a173 4
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CXXOPTS)
CXXTHREADFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CXXTHREADOPTS)
CXXSIMPARAMFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT) $(CXXSIMPARAMOPTS)
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(TCL) $(FFT)
@


1.1086
log
@Added CXXSIMPARAMOPTS, to allow the T3E to compile
@
text
@a90 1
	$(DSTDIR)/IntTree.o \
@


1.1085
log
@Cleaned up Makefile.
@
text
@d173 1
d356 1
@


1.1084
log
@Cleaned up compilation.
@
text
@d4 1
a4 5
#####
# Directories
#####

# source directory
a5 1
# destination directory (binaries) -- currently, MUST be .
a6 1
# temp include directory for .decl.h and .def.h files
d8 3
d12 3
a14 16
#####
# definitions for Charm routines
#####

# CHARM is platform dependent
CHARMC = $(CHARM)/bin/charmc $(PURIFY)
CHARMXI = $(CHARM)/bin/charmc $(PURIFY)


#####
# definitions for (D)PMTA routines
#####

DPMTADIR=dpmta-2.6
DPMTAINCL=-I$(DPMTADIR)/mpole -I$(DPMTADIR)/src
DPMTALIB=-L$(DPMTADIR)/mpole -L$(DPMTADIR)/src -ldpmta2 -lmpole
d17 1
a17 1
DPMTALIBS=$(DPMTADIR)/mpole/libmpole.a $(DPMTADIR)/src/libdpmta2.a
d19 1
a19 6

#####
# definitions for DPME routines
#####

DPMEDIR=dpme2
a25 26

######
## definitions for PVM routines
######

PVMDIR=pvm3
PVMLIB=-L$(PVMDIR) -lpvmc
PVM=-I$(PVMDIR)
PVMLIBS=pvm3/libpvmc.a


######
## Libraries we may have changed
######

LIBS = $(DPMTALIBS) $(PVMLIBS) $(DPMELIBS)


# CXX is platform dependent
INCLUDE = $(CHARM)/include
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(PVM) $(TCL) $(FFT) $(CXXOPTS) $(NOWARN) $(NAMDFLAGS)
CXXTHREADFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(PVM) $(TCL) $(FFT) $(CXXTHREADOPTS) $(NOWARN) $(NAMDFLAGS)
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(PVM) $(TCL) $(FFT) $(NOWARN) $(NAMDFLAGS)

DEPENDFILE = Make.depends

d135 1
d162 13
d183 1
a183 1
	"-I$(INCLUDE) -I$(INCDIR) -I$(SRCDIR) $(CXXOPTS) $(LDOPTS)" \
a187 1
	$(PVMLIB) \
a205 2
# Now sit back, have a coke, and relax.

a206 3
	cd $(PVMDIR) ; $(MAKE) CHARM=$(CHARM) ; cd ..
	cd $(DPMTADIR) ; $(MAKE) CHARM=$(CHARM) ; cd ..
	cd $(DPMEDIR) ; $(MAKE) CHARM=$(CHARM) ; cd ..
d208 1
a208 1
	"-I$(INCLUDE) -I$(SRCDIR) $(CXXOPTS) " \
a212 1
	$(PVMLIB) \
a215 2
# Now sit back, have a coke, and relax.

d225 1
a225 1
pvm3/libpvmc.a:
d327 2
a377 2
accesslist:
	cvs admin -aari,brunner,jim,milind,nealk .
@


1.1083
log
@Added internal PUB3DFFT package.
@
text
@d270 7
@


1.1082
log
@Eliminated MDComm from all files and Makefiles
@
text
@d179 1
d403 1
a403 1
	rm -rf ptrepository Templates.DB $(DSTDIR) $(INCDIR)
@


1.1081
log
@The -dalign flag (part of -fast) was screwing up threads in ReductionMgr.C
@
text
@d67 3
a69 3
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(PVM) $(MDCOMM) $(TCL) $(FFT) $(CXXOPTS) $(NOWARN) $(NAMDFLAGS)
CXXTHREADFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(PVM) $(MDCOMM) $(TCL) $(FFT) $(CXXTHREADOPTS) $(NOWARN) $(NAMDFLAGS)
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(PVM) $(MDCOMM) $(TCL) $(FFT) $(NOWARN) $(NAMDFLAGS)
a78 1
	$(DSTDIR)/mdcomm.o \
a107 1
	$(DSTDIR)/ComputeMDComm.o \
a220 1
	$(MDCOMMLIB) \
a251 1
	$(MDCOMMLIB) \
@


1.1080
log
@Incorporated Justin's interactive MD code.
@
text
@d390 1
@


1.1079
log
@Added ccs interface file
@
text
@d105 1
d137 1
d180 3
a182 2
	$(DSTDIR)/WorkDistrib.o

@


1.1078
log
@Undid attempt to create inc and obj dirs.
@
text
@d123 1
@


1.1077
log
@Now builds inc and obj directories when needed.
@
text
@d273 1
a273 1
$(INCDIR)/BroadcastMgr.decl.h:	$(INCDIR) $(SRCDIR)/BroadcastMgr.ci
d277 1
a277 1
$(INCDIR)/BroadcastMgr.def.h:	$(INCDIR) $(SRCDIR)/BroadcastMgr.ci
d281 1
a281 1
$(INCDIR)/CollectionMaster.decl.h:	$(INCDIR) $(SRCDIR)/CollectionMaster.ci
d285 1
a285 1
$(INCDIR)/CollectionMaster.def.h:	$(INCDIR) $(SRCDIR)/CollectionMaster.ci
d289 1
a289 1
$(INCDIR)/CollectionMgr.decl.h:	$(INCDIR) $(SRCDIR)/CollectionMgr.ci
d293 1
a293 1
$(INCDIR)/CollectionMgr.def.h:	$(INCDIR) $(SRCDIR)/CollectionMgr.ci
d297 1
a297 1
$(INCDIR)/ComputeMgr.decl.h:	$(INCDIR) $(SRCDIR)/ComputeMgr.ci
d301 1
a301 1
$(INCDIR)/ComputeMgr.def.h:	$(INCDIR) $(SRCDIR)/ComputeMgr.ci
d305 1
a305 1
$(INCDIR)/LdbCoordinator.decl.h:	$(INCDIR) $(SRCDIR)/LdbCoordinator.ci
d309 1
a309 1
$(INCDIR)/LdbCoordinator.def.h:	$(INCDIR) $(SRCDIR)/LdbCoordinator.ci
d313 1
a313 1
$(INCDIR)/Node.decl.h:	$(INCDIR) $(SRCDIR)/Node.ci
d317 1
a317 1
$(INCDIR)/Node.def.h:	$(INCDIR) $(SRCDIR)/Node.ci
d321 1
a321 1
$(INCDIR)/PatchMgr.decl.h:	$(INCDIR) $(SRCDIR)/PatchMgr.ci
d325 1
a325 1
$(INCDIR)/PatchMgr.def.h:	$(INCDIR) $(SRCDIR)/PatchMgr.ci
d329 1
a329 1
$(INCDIR)/ProxyMgr.decl.h:	$(INCDIR) $(SRCDIR)/ProxyMgr.ci
d333 1
a333 1
$(INCDIR)/ProxyMgr.def.h:	$(INCDIR) $(SRCDIR)/ProxyMgr.ci
d337 1
a337 1
$(INCDIR)/ReductionMgr.decl.h:	$(INCDIR) $(SRCDIR)/ReductionMgr.ci
d341 1
a341 1
$(INCDIR)/ReductionMgr.def.h:	$(INCDIR) $(SRCDIR)/ReductionMgr.ci
d345 1
a345 1
$(INCDIR)/WorkDistrib.decl.h:	$(INCDIR) $(SRCDIR)/WorkDistrib.ci
d349 1
a349 1
$(INCDIR)/WorkDistrib.def.h:	$(INCDIR) $(SRCDIR)/WorkDistrib.ci
d353 1
a353 1
$(INCDIR)/main.decl.h:	$(INCDIR) $(SRCDIR)/main.ci
d357 1
a357 1
$(INCDIR)/main.def.h:	$(INCDIR) $(SRCDIR)/main.ci
d386 1
a386 1
	    -e "s/\:/\: obj/" $(DEPENDFILE) > $(DEPENDFILE).sed; \
@


1.1076
log
@Incorporated Justin's faster PME code along side DPME.
@
text
@d273 1
a273 1
$(INCDIR)/BroadcastMgr.decl.h:	$(SRCDIR)/BroadcastMgr.ci
d277 1
a277 1
$(INCDIR)/BroadcastMgr.def.h:	$(SRCDIR)/BroadcastMgr.ci
d281 1
a281 1
$(INCDIR)/CollectionMaster.decl.h:	$(SRCDIR)/CollectionMaster.ci
d285 1
a285 1
$(INCDIR)/CollectionMaster.def.h:	$(SRCDIR)/CollectionMaster.ci
d289 1
a289 1
$(INCDIR)/CollectionMgr.decl.h:	$(SRCDIR)/CollectionMgr.ci
d293 1
a293 1
$(INCDIR)/CollectionMgr.def.h:	$(SRCDIR)/CollectionMgr.ci
d297 1
a297 1
$(INCDIR)/ComputeMgr.decl.h:	$(SRCDIR)/ComputeMgr.ci
d301 1
a301 1
$(INCDIR)/ComputeMgr.def.h:	$(SRCDIR)/ComputeMgr.ci
d305 1
a305 1
$(INCDIR)/LdbCoordinator.decl.h:	$(SRCDIR)/LdbCoordinator.ci
d309 1
a309 1
$(INCDIR)/LdbCoordinator.def.h:	$(SRCDIR)/LdbCoordinator.ci
d313 1
a313 1
$(INCDIR)/Node.decl.h:	$(SRCDIR)/Node.ci
d317 1
a317 1
$(INCDIR)/Node.def.h:	$(SRCDIR)/Node.ci
d321 1
a321 1
$(INCDIR)/PatchMgr.decl.h:	$(SRCDIR)/PatchMgr.ci
d325 1
a325 1
$(INCDIR)/PatchMgr.def.h:	$(SRCDIR)/PatchMgr.ci
d329 1
a329 1
$(INCDIR)/ProxyMgr.decl.h:	$(SRCDIR)/ProxyMgr.ci
d333 1
a333 1
$(INCDIR)/ProxyMgr.def.h:	$(SRCDIR)/ProxyMgr.ci
d337 1
a337 1
$(INCDIR)/ReductionMgr.decl.h:	$(SRCDIR)/ReductionMgr.ci
d341 1
a341 1
$(INCDIR)/ReductionMgr.def.h:	$(SRCDIR)/ReductionMgr.ci
d345 1
a345 1
$(INCDIR)/WorkDistrib.decl.h:	$(SRCDIR)/WorkDistrib.ci
d349 1
a349 1
$(INCDIR)/WorkDistrib.def.h:	$(SRCDIR)/WorkDistrib.ci
d353 1
a353 1
$(INCDIR)/main.decl.h:	$(SRCDIR)/main.ci
d357 1
a357 1
$(INCDIR)/main.def.h:	$(SRCDIR)/main.ci
d386 1
a386 1
	    $(DEPENDFILE) > $(DEPENDFILE).sed; \
@


1.1075
log
@Added simplified interface to ComputeGlobal mechanism.
@
text
@d67 3
a69 3
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(PVM) $(MDCOMM) $(TCL) $(CXXOPTS) $(NOWARN) $(NAMDFLAGS)
CXXTHREADFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(PVM) $(MDCOMM) $(TCL) $(CXXTHREADOPTS) $(NOWARN) $(NAMDFLAGS)
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(PVM) $(MDCOMM) $(TCL) $(NOWARN) $(NAMDFLAGS)
d115 2
d155 5
@


1.1074
log
@Added basic scripting.
@
text
@d102 1
d106 1
@


1.1073
log
@Added utilities to deal with DCD file formats.
@
text
@d158 1
@


1.1072
log
@Changes for new charm version
@
text
@d219 9
@


1.1071
log
@Generalized FFTW to FFT.
@
text
@d12 1
a12 1
# temp include directory for .top.h and .bot.h files
d172 22
a193 22
		$(INCDIR)/BroadcastMgr.top.h \
		$(INCDIR)/BroadcastMgr.bot.h \
		$(INCDIR)/CollectionMaster.top.h \
		$(INCDIR)/CollectionMaster.bot.h \
		$(INCDIR)/CollectionMgr.top.h \
		$(INCDIR)/CollectionMgr.bot.h \
		$(INCDIR)/ComputeMgr.top.h \
		$(INCDIR)/ComputeMgr.bot.h \
		$(INCDIR)/LdbCoordinator.top.h \
		$(INCDIR)/LdbCoordinator.bot.h \
		$(INCDIR)/Node.top.h \
		$(INCDIR)/Node.bot.h \
		$(INCDIR)/PatchMgr.top.h \
		$(INCDIR)/PatchMgr.bot.h \
		$(INCDIR)/ProxyMgr.top.h \
		$(INCDIR)/ProxyMgr.bot.h \
		$(INCDIR)/ReductionMgr.top.h \
		$(INCDIR)/ReductionMgr.bot.h \
		$(INCDIR)/WorkDistrib.top.h \
		$(INCDIR)/WorkDistrib.bot.h \
		$(INCDIR)/main.top.h \
		$(INCDIR)/main.bot.h
d203 1
a203 1
	"-I$(INCLUDE) -I$(SRCDIR) $(CXXOPTS) " \
d252 1
a252 1
MOVECIFILES = $(MOVE) $(SRCDIR)/*.top.h $(SRCDIR)/*.bot.h $(INCDIR)
d254 1
a254 1
$(INCDIR)/BroadcastMgr.top.h:	$(SRCDIR)/BroadcastMgr.ci
d258 1
a258 1
$(INCDIR)/BroadcastMgr.bot.h:	$(SRCDIR)/BroadcastMgr.ci
d262 1
a262 1
$(INCDIR)/CollectionMaster.top.h:	$(SRCDIR)/CollectionMaster.ci
d266 1
a266 1
$(INCDIR)/CollectionMaster.bot.h:	$(SRCDIR)/CollectionMaster.ci
d270 1
a270 1
$(INCDIR)/CollectionMgr.top.h:	$(SRCDIR)/CollectionMgr.ci
d274 1
a274 1
$(INCDIR)/CollectionMgr.bot.h:	$(SRCDIR)/CollectionMgr.ci
d278 1
a278 1
$(INCDIR)/ComputeMgr.top.h:	$(SRCDIR)/ComputeMgr.ci
d282 1
a282 1
$(INCDIR)/ComputeMgr.bot.h:	$(SRCDIR)/ComputeMgr.ci
d286 1
a286 1
$(INCDIR)/LdbCoordinator.top.h:	$(SRCDIR)/LdbCoordinator.ci
d290 1
a290 1
$(INCDIR)/LdbCoordinator.bot.h:	$(SRCDIR)/LdbCoordinator.ci
d294 1
a294 1
$(INCDIR)/Node.top.h:	$(SRCDIR)/Node.ci
d298 1
a298 1
$(INCDIR)/Node.bot.h:	$(SRCDIR)/Node.ci
d302 1
a302 1
$(INCDIR)/PatchMgr.top.h:	$(SRCDIR)/PatchMgr.ci
d306 1
a306 1
$(INCDIR)/PatchMgr.bot.h:	$(SRCDIR)/PatchMgr.ci
d310 1
a310 1
$(INCDIR)/ProxyMgr.top.h:	$(SRCDIR)/ProxyMgr.ci
d314 1
a314 1
$(INCDIR)/ProxyMgr.bot.h:	$(SRCDIR)/ProxyMgr.ci
d318 1
a318 1
$(INCDIR)/ReductionMgr.top.h:	$(SRCDIR)/ReductionMgr.ci
d322 1
a322 1
$(INCDIR)/ReductionMgr.bot.h:	$(SRCDIR)/ReductionMgr.ci
d326 1
a326 1
$(INCDIR)/WorkDistrib.top.h:	$(SRCDIR)/WorkDistrib.ci
d330 1
a330 1
$(INCDIR)/WorkDistrib.bot.h:	$(SRCDIR)/WorkDistrib.ci
d334 1
a334 1
$(INCDIR)/main.top.h:	$(SRCDIR)/main.ci
d338 1
a338 1
$(INCDIR)/main.bot.h:	$(SRCDIR)/main.ci
@


1.1070
log
@Reduced optimization for full direct code because of strange errors.
@
text
@d211 1
a211 1
	$(FFTWLIB)
d234 1
a234 1
	$(FFTWLIB)
@


1.1069
log
@Added FFTW library flag.
@
text
@d366 1
@


1.1068
log
@Moved "include Make.charm" out of Makearch and into Makefile.
@
text
@d210 2
a211 1
	$(TCLLIB)
d233 2
a234 1
	$(TCLLIB)
@


1.1067
log
@Cleaned up building process.  Now automatically creates cifiles.
@
text
@d1 1
@


1.1066
log
@initial check in of code for fixed and forcing restraints
-Dave Hurwitz
@
text
@d11 1
a11 1
# temp include directory for cifiles
a34 1

d70 1
a70 1
.SUFFIXES: 	.ci
d72 1
a72 1
DEPENDFILE = Make.depends
d168 27
a194 1
#Compute.ci - nolonger necessary(?)
d196 3
a198 4
INTERFACES = main.ci Node.ci WorkDistrib.ci PatchMgr.ci \
		ComputeMgr.ci ProxyMgr.ci ReductionMgr.ci \
		CollectionMgr.ci CollectionMaster.ci BroadcastMgr.ci \
		LdbCoordinator.ci
d211 6
d247 91
a337 6
cifiles:	$(INCDIR) $(DSTDIR)
	for i in $(INTERFACES); do \
	   $(CHARMXI) $(SRCDIR)/$$i; \
	done;
	$(MOVE) $(SRCDIR)/*.top.h $(INCDIR)
	$(MOVE) $(SRCDIR)/*.bot.h $(INCDIR)
d342 1
a342 1
depends: cifiles $(DSTDIR) $(DEPENDSFILE)
d366 2
a367 2
Make.depends:
	touch $(DEPENDSFILE)
a370 8
#$(INTERFACES:.ci=.top.h):	$(INCDIR) $$(@@:.top.h=.ci)
#	$(CHARMXI) $?
#	$(MOVE) $(SRCDIR)/*.top.h $(INCDIR)

#$(INTERFACES:.ci=.bot.h):	$(INCDIR) $$(@@:.bot.h=.ci)
#	$(CHARMXI) $?
#	$(MOVE) $(SRCDIR)/*.bot.h $(INCDIR)

d378 1
a378 3
	rm -rf ptrepository
	rm -rf $(DSTDIR)
	rm -f namd2
d384 1
a384 4
	rm -rf $(INCDIR)
	rm -f *.depends
	# allow for the makefile to continue to work
	touch $(DEPENDFILE)
@


1.1065
log
@Added ComputeMDComm for forces from VMD.
@
text
@d120 8
@


1.1064
log
@Allowed to compile thread files -g if compiler causes errors.
@
text
@d106 1
@


1.1063
log
@Fixed up MDCOMM code.
@
text
@a56 13
######
## definitions for TCL interface
######
##
## MOVED TO Makearch.* !!!
##
######
##
#TCLDIR=/usr/local
#TCLINCL=-I$(TCLDIR)/include
#TCLLIB=-L$(TCLDIR)/lib -ltclx -ltcl
#TCLFLAGS=-DNAMD_TCL
#TCL=$(TCLINCL) $(TCLFLAGS)
d68 1
d233 8
a240 1
	done;
@


1.1062
log
@Finished incorporating DPME.
@
text
@d80 2
a81 2
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(PVM) $(TCL) $(CXXOPTS) $(NOWARN) $(NAMDFLAGS)
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(DPME) $(PVM) $(TCL) $(NOWARN) $(NAMDFLAGS)
d91 1
d187 1
d203 1
@


1.1061
log
@Added DPME.
@
text
@d105 1
@


1.1060
log
@Added TestController and TestSequencer.
@
text
@d41 2
a42 2
DPMEINCL=-I$(DPMEDIR)/include
DPMELIB=-L$(DPMEDIR) -ldpme2 -lmpole
d45 1
a45 1
#DPMELIBS= dpme2/libdpme2.a
d80 2
a81 2
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(PVM) $(TCL) $(CXXOPTS) $(NOWARN) $(NAMDFLAGS)
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(PVM) $(TCL) $(NOWARN) $(NAMDFLAGS)
d104 1
d183 1
d192 1
d198 1
d210 1
a210 1
dpme2/libdpme2.a:
@


1.1059
log
@Added class ComputeFreeEnergy.
@
text
@d164 2
@


1.1058
log
@Split ComputeGlobal into different classes and files.
@
text
@d105 1
@


1.1057
log
@Moved TCL flags and variables to the Makearch files, because the T3E
doesn't have TCL, so I needed to turn it off depending on machine-type.
@
text
@d110 1
d123 1
@


1.1056
log
@Added tclx library.
@
text
@a56 1

d60 10
a69 7

TCLDIR=/usr/local
TCLINCL=-I$(TCLDIR)/include
TCLLIB=-L$(TCLDIR)/lib -ltclx -ltcl
TCLFLAGS=-DNAMD_TCL
TCL=$(TCLINCL) $(TCLFLAGS)

@


1.1055
log
@added ComputeSMD.o, SMD.o, SMDMsgs.o
@
text
@d62 5
a66 5
#TCLDIR=/usr/local
#TCLINCL=-I$(TCLDIR)/include
#TCLLIB=-L$(TCLDIR)/lib -ltcl
#TCLFLAGS=-DNAMD_TCL
#TCL=$(TCLINCL) $(TCLFLAGS)
@


1.1054
log
@Made namd2 to compile, link and run under linux. Merged Templates and src
directoriies, and removed separate definition and declaration files for
templates.
@
text
@d118 1
d156 2
@


1.1053
log
@Added Tcl interface for calculating forces.
@
text
@d62 5
a66 5
TCLDIR=/usr/local
TCLINCL=-I$(TCLDIR)/include
TCLLIB=-L$(TCLDIR)/lib -ltcl
TCLFLAGS=-DNAMD_TCL
TCL=$(TCLINCL) $(TCLFLAGS)
d78 1
a78 1
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(SRCDIR)/Templates -I$(INCDIR) $(DPMTA) $(PVM) $(TCL) $(CXXOPTS) $(NOWARN) $(NAMDFLAGS)
d166 1
a166 16
TEMPLATES = \
	$(SRCDIR)/ComputeHomeTuples.C \
	$(SRCDIR)/PositionBox.C \
	$(SRCDIR)/PositionOwnerBox.C \
	$(SRCDIR)/BroadcastObject.C \
	$(SRCDIR)/Templates/Box.C \
	$(SRCDIR)/Templates/ObjectArena.C \
	$(SRCDIR)/Templates/OwnerBox.C \
	$(SRCDIR)/Templates/ResizeArray.C \
	$(SRCDIR)/Templates/ResizeArrayRaw.C \
	$(SRCDIR)/Templates/SortableResizeArray.C \
	$(SRCDIR)/Templates/SortedArray.C \
	$(SRCDIR)/Templates/UniqueSetRaw.C \
	$(SRCDIR)/Templates/UniqueSortedArray.C

namd2:	$(INCDIR) $(DSTDIR) $(OBJS) $(TEMPLATES) $(LIBS)
d168 1
a168 1
	"-I$(INCLUDE) -I$(SRCDIR) -I$(SRCDIR)/Templates $(CXXOPTS) " \
d177 1
a177 1
projections:	$(INCDIR) $(DSTDIR) $(OBJS) $(TEMPLATES) $(LIBS)
d181 1
a181 1
	"-I$(INCLUDE) -I$(SRCDIR) -I$(SRCDIR)/Templates $(CXXOPTS) " \
@


1.1052
log
@Made NAMD to run on shared memory machines.
@
text
@d59 11
d78 2
a79 2
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(SRCDIR)/Templates -I$(INCDIR) $(DPMTA) $(PVM) $(CXXOPTS) $(NOWARN) $(NAMDFLAGS)
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(PVM) $(NOWARN) $(NAMDFLAGS)
d107 2
d155 1
d187 2
a188 1
	$(PVMLIB)
d200 2
a201 1
	$(PVMLIB)
@


1.1051
log
@Modified to enbale linking without DPMTA.
@
text
@d108 1
d132 1
@


1.1050
log
@Added a make projections target, and removed CYCLE_BARRRIER flag on T3E
@
text
@d32 2
d45 1
d55 1
d62 1
a62 2
LIBS = $(DPMTADIR)/mpole/libmpole.a $(DPMTADIR)/src/libdpmta2.a pvm3/libpvmc.a
# dpme2/libdpme2.a
a85 1
	$(DSTDIR)/CommunicateConverse.o \
d116 1
a116 3
	$(DSTDIR)/Message.o \
	$(DSTDIR)/MessageManager.o \
	$(DSTDIR)/MessageQueue.o \
a165 2
	cd $(PVMDIR) ; $(MAKE) CHARM=$(CHARM) ; cd ..
	cd $(DPMTADIR) ; $(MAKE) CHARM=$(CHARM) ; cd ..
@


1.1049
log
@Fixed Makefiles to include arch params from a single file.
@
text
@d177 12
@


1.1048
log
@Changes to work with DPMTA-2.6
@
text
@a13 1

d64 2
a65 2
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(SRCDIR)/Templates -I$(INCDIR) $(DPMTA) $(PVM) $(CXXOPTS) $(NOWARN)
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(PVM) $(NOWARN)
a130 1
	$(DSTDIR)/Priorities.o \
d173 3
a175 2
	$(PVMLIB) \
	# Now sit back, have a coke, and relax.
d178 1
a178 1
	cd $(DPMTADIR) ; $(MAKE) CHARM=$(CHARM) ; cd ..
d181 1
a181 1
	cd $(DPMTADIR) ; $(MAKE) CHARM=$(CHARM) ; cd ..
d184 1
a184 1
	cd $(DPMEDIR) ; $(MAKE) CHARM=$(CHARM) ; cd ..
d187 1
a187 1
	cd $(PVMDIR) ; $(MAKE) CHARM=$(CHARM) ; cd ..
@


1.1047
log
@Made NAMD2 to link on Solaris machines.
@
text
@a12 3
# Libraries we may have changed
LIBS = dpmta2/mpole/libmpole.a dpmta2/src/libdpmta2.a pvm3/libpvmc.a
# dpme2/libdpme2.a
d28 3
a30 3
DPMTADIR=dpmta2
DPMTAINCL=-I$(DPMTADIR)/include
DPMTALIB=-L$(DPMTADIR) -ldpmta2 -lmpole
d55 8
d178 1
a178 1
dpmta2/mpole/libmpole.a:
d181 1
a181 1
dpmta2/src/libdpmta2.a:
d212 1
a212 1
	      $(ECHO) "	$$(CXX) $$(CXXFLAGS)" -o $$i -c \
@


1.1046
log
@Restructured the Makefile and Makearch structure.
@
text
@d207 1
a207 1
	      $(ECHO) '\t$$(CXX) $$(CXXFLAGS)' -o $$i -c \
@


1.1045
log
@Ported NAMD2 to SP3. The SP specific code is within #ifdef SP2
and #endif's.
@
text
@d1 1
d4 1
a4 1
## Define your architecture
a5 6
# ARCH = Origin2000
ARCH = SP3
# ARCH = HPUX9
# ARCH = HPUX10
# ARCH = g++
include Makearch.$(ARCH)
a6 3
#####
# Directories
#####
d21 1
d26 1
d30 1
d36 2
d41 1
d47 2
d52 1
d206 1
a206 1
	      $(SRCDIR)/dc.pl $(INCLUDE) /usr/include /usr/local >> $(DEPENDFILE); \
@


1.1044
log
@Made namd2 to work with Origin2000: Again...
@
text
@d5 2
a6 1
ARCH = Origin2000
@


1.1043
log
@Added ComputeRestraints.o (harmonic restraints)
@
text
@d5 2
a6 2
# ARCH = Origin2000
ARCH = HPUX9
@


1.1042
log
@Make clean now cleans the PVM directory.
(Who removed it!)
@
text
@d96 1
@


1.1041
log
@Added RecBisection for initial patch distrib
@
text
@d233 1
@


1.1040
log
@Added AlgSeven.C (Alg7.C file name does not work, due to number).
@
text
@d70 1
a71 1
	$(DSTDIR)/AlgSeven.o \
d128 1
@


1.1039
log
@Added Priorities.C to set a static variable numBits
@
text
@d71 1
@


1.1038
log
@Added Rebalancer and associated files
@
text
@d123 1
@


1.1037
log
@Got NAMD2 to run on Origin2000.
Included definitions of class static variables in C files.
Fixed alignment bugs by using memcpy instead of assignment in
pack and unpack.
@
text
@d98 1
d125 1
d127 1
d129 1
@


1.1036
log
@Removed dpme2.a from the compilation (for now).
@
text
@d5 1
d58 1
a58 1
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(PVM) $(CXXOPTS) $(NOWARN)
d156 1
a156 1
	"-I $(INCLUDE) -I $(SRCDIR) $(CXXOPTS) " \
d207 7
a213 7
$(INTERFACES:.ci=.top.h):	$(INCDIR) $$(@@:.top.h=.ci)
	$(CHARMXI) $?
	$(MOVE) $(SRCDIR)/*.top.h $(INCDIR)

$(INTERFACES:.ci=.bot.h):	$(INCDIR) $$(@@:.bot.h=.ci)
	$(CHARMXI) $?
	$(MOVE) $(SRCDIR)/*.bot.h $(INCDIR)
@


1.1035
log
@Makefile which includes architecure definitions
@
text
@d20 2
a21 1
LIBS = dpmta2/mpole/libmpole.a dpmta2/src/libdpmta2.a pvm3/libpvmc.a dpme2/libdpme2.a
@


1.1034
log
@Changed so CHARM directory only needs to be defined in 1 place.
@
text
@d3 6
a8 24
## Choose your favorite Compiler options
####
CXXOPTS = -O -DGLOBALS
#CXXOPTS = +O2
#CXXOPTS = +O3
#CXXOPTS = +O3 +DAK220 +DSK220 -G +Oinlinebudget=500 +Olibcalls
#CXXOPTS = +O3 +DAK220 +DSK220 -G
#CXXOPTS = +O3 +DAK460 +DSK460
# this one below leads to numerical changes!
#CXXOPTS = +O3 -G -z -ptn +Oentrysched +Ofastaccess +Onofltacc +Oregionsched
#CXXOPTS = +O3 -G -z -ptn +Oentrysched
#CXXOPTS = +O3 -G
#CXXOPTS = +O3 -z
#CXXOPTS = -g -v -z -G
#CXXOPTS = -g -v
#CXXOPTS = -g 

#####
# Flags
#####
# uncomment for no warnings during compile
#NOWARN=-w
# uncomment for purify during compile
# PURIFY=-purify
d26 1
a26 2
CHARM = /Projects/l1/namd.2.0/charm
# CHARM = /Home/p1/milind/charm/net-hp
d54 1
a54 2
CXX = CC -Aa -D_HPUX_SOURCE
# CXX = g++ -D_HPUX_SOURCE
a61 3
ECHO = echo
MOVE = mv
COPY = cp
@


1.1033
log
@make depends now works on io
@
text
@d5 2
a6 1
#CXXOPTS = -O
d14 1
a14 1
CXXOPTS = +O3
d26 1
a26 1
#PURIFY=-purify
d45 1
d74 2
a75 1
INCLUDE = /Projects/l1/namd.2.0/charm/include
@


1.1032
log
@Added LdbCoordinator.[C,ci]
@
text
@d13 1
a13 1
#CXXOPTS = +O3 -G
d17 1
a17 1
CXXOPTS = -g 
d215 2
a216 2
	      $(ECHO) "\t$$(CXX) $$(CXXFLAGS) -o "$$i" -c" \
	        "$$(SRCDIR)/"`basename $$i | awk -F. '{print $$1".C"}'` \
@


1.1031
log
@Option changes
@
text
@d13 1
a13 1
CXXOPTS = +O3 -G
d17 1
a17 1
#CXXOPTS = -g 
d121 1
d152 2
a153 1
		CollectionMgr.ci CollectionMaster.ci BroadcastMgr.ci
@


1.1030
log
@No major changes
@
text
@d7 2
a8 1
CXXOPTS = +O3 +DAK220 +DSK220 -G
d13 1
a13 1
#CXXOPTS = +O3 -G
@


1.1029
log
@Added ComputeSphericalBC.
@
text
@d7 2
a8 2
#CXXOPTS = +O3 +DAK220 +DSK220
CXXOPTS = +O3 +DAK460 +DSK460
d16 1
d88 2
d150 1
a150 1
		CollectionMgr.ci CollectionMaster.ci
d156 1
@


1.1028
log
@Updating makefile
@
text
@d109 1
@


1.1027
log
@Did cleanups and speedups in preparation for virial calculation.
Fixed minor bug which resulted in incorrect energies for excluded
pairs which were outside of the cutoff radius (VERY rare).
@
text
@d35 1
a35 1
LIBS = dpmta2/mpole/libmpole.a dpmta2/src/libdpmta2.a pvm3/libpvmc.a
d53 8
d179 3
d235 2
a236 1
#	cd $(DPMTADIR) ; $(MAKE) clean ; cd ..
@


1.1026
log
@Added ComputeCylindricalBC to list.
@
text
@d7 2
a8 2
CXXOPTS = +O3 +DAK220 +DSK220
#CXXOPTS = +O3 +DAK460 +DSK460
@


1.1025
log
@Just optimization flag
@
text
@d6 3
a8 1
#CXXOPTS = -O +DAK460 +DSK460
d12 1
a12 1
CXXOPTS = +O3
d86 1
@


1.1024
log
@Added dependencies for new templates.
@
text
@d10 1
a10 1
CXXOPTS = +O3 -G 
d13 1
a13 1
#CXXOPTS = -g
d19 1
a19 1
NOWARN=-w
@


1.1023
log
@*** empty log message ***
@
text
@d142 1
d145 1
d148 1
@


1.1022
log
@No change - my opts
@
text
@d10 2
a11 2
#CXXOPTS = +O3 -G -z
CXXOPTS = +O3 -z
@


1.1021
log
@Removed Compute.ci
@
text
@d3 21
a34 7
#####
# Flags
#####
# uncomment for no warnings during compile
NOWARN=-w
# uncomment for purify during compile
#PURIFY=-purify
a57 11
#####
## Choose your favorite Compiler options
####
#CXXOPTS = -O
# this one below leads to numerical changes!
#CXXOPTS = +O3 -G -z -ptn +Oentrysched +Ofastaccess +Onofltacc +Oregionsched
#CXXOPTS = +O3 -G -z -ptn +Oentrysched
#CXXOPTS = +O3 -G -z
CXXOPTS = +O3 -z
#CXXOPTS = -O +DAK460 +DSK460
#CXXOPTS = -g
@


1.1020
log
@Added new file NamdOneTools.C -
tested out some compiler flags for speed
Fixed up a few subsidiary builds (passing down flags etc)
@
text
@d18 1
a18 1
#NOWARN=-w
d51 2
a52 1
CXXOPTS = +O3 -G -z
d128 3
a130 1
INTERFACES = main.ci Node.ci WorkDistrib.ci PatchMgr.ci Compute.ci \
@


1.1019
log
@Turned on optimization
@
text
@d47 5
a51 2
CXXOPTS = -O
#CXXOPTS = +O3 -G -z 
d109 1
@


1.1018
log
@Added PVM includes to g++ calls during make depends.
@
text
@d47 1
a47 1
#CXXOPTS = -O
d50 1
a50 1
CXXOPTS = -g
@


1.1017
log
@Tried to get dpmta/pvm changes to compile in a general (but hack) way
@
text
@d55 1
a55 1
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(NOWARN)
@


1.1016
log
@Added CHARM= to the specific library calls.
@
text
@d26 2
a27 2
CHARMC = /Projects/l1/namd.2.0/charm/bin/charmc $(PURIFY)
CHARMXI = /Projects/l1/namd.2.0/charm/bin/charmc $(PURIFY)
d44 8
a51 3
#CXXOPTS = -g
CXXOPTS = -O 
# CXXOPTS = -O +DAK460 +DSK460
d140 1
a140 1
	cd $(DPMTADIR) ; $(MAKE) ; cd ..
@


1.1015
log
@Fixed problems compiling Charm version of pvm.
@
text
@d145 1
a145 1
	cd $(DPMTADIR) ; $(MAKE) ; cd ..
d148 1
a148 1
	cd $(DPMTADIR) ; $(MAKE) ; cd ..
d151 1
a151 1
	cd $(PVMDIR) ; $(MAKE) ; cd ..
@


1.1014
log
@Added accesslist target for adding new people
@
text
@d25 1
a43 1
# CXXOPTS = -O
d134 1
a134 1
	cd $(PVMDIR) ; $(MAKE) ; cd ..
@


1.1013
log
@Namd2 depends on libs (to make Robbert happy)
@
text
@d211 2
@


1.1012
log
@Someone else edited my makefile!  Had to fix it again!
@
text
@d133 1
a133 1
namd2:	$(INCDIR) $(DSTDIR) $(OBJS) $(TEMPLATES)
d143 9
@


1.1011
log
@Added dependencies for dpmta2 and pvmc libraries
@
text
@d29 1
a29 1
# definitions for PMTA routines
d133 2
a134 1
namd2:	$(INCDIR) $(DSTDIR) $(OBJS) $(TEMPLATES) $(LIBS)
a135 1
	cd $(PVMDIR) ; $(MAKE) ; cd ..
@


1.1010
log
@Uncommented the "cd ... make" for PVM and DPMTA.  Ugh.
@
text
@d11 2
d45 1
a45 1
CXXOPTS = -O -G
d133 1
a133 1
namd2:	$(INCDIR) $(DSTDIR) $(OBJS) $(TEMPLATES)
@


1.1009
log
@Turned DPMTA and PVM back on...
@
text
@d132 2
a133 2
#	cd $(DPMTADIR) ; $(MAKE) ; cd ..
#	cd $(PVMDIR) ; $(MAKE) ; cd ..
@


1.1008
log
@Commented out dpmta
@
text
@d29 5
a33 5
#DPMTADIR=dpmta2
#DPMTAINCL=-I$(DPMTADIR)/include
#DPMTALIB=-L$(DPMTADIR) -ldpmta2 -lmpole
#DPMTAFLAGS=-DDPMTA
#DPMTA=$(DPMTAINCL) $(DPMTAFLAGS)
d37 3
a39 3
#PVMDIR=pvm3
#PVMLIB=-L$(PVMDIR) -lpvmc
#PVM=-I$(PVMDIR)
@


1.1007
log
@Modified for new DPMTA...
@
text
@d29 5
a33 5
DPMTADIR=dpmta2
DPMTAINCL=-I$(DPMTADIR)/include
DPMTALIB=-L$(DPMTADIR) -ldpmta2 -lmpole
DPMTAFLAGS=-DDPMTA
DPMTA=$(DPMTAINCL) $(DPMTAFLAGS)
d37 3
a39 3
PVMDIR=pvm3
PVMLIB=-L$(PVMDIR) -lpvmc
PVM=-I$(PVMDIR)
d42 2
a43 1
CXXOPTS = -g
d95 1
d132 3
a134 3
	cd $(DPMTADIR) ; $(MAKE) ; cd ..
	cd $(PVMDIR) ; $(MAKE) ; cd ..
	$(CHARMC) -ld++-option \
d192 1
a192 1
	cd $(DPMTADIR) ; $(MAKE) clean ; cd ..
@


1.1006
log
@Small change to avoid PVMLIBDIR conflict with shell when commented out.
@
text
@d29 5
a33 5
DPMTADIR=dpmta
#PMTAINCL=-I$(DPMTADIR)
#PMTALIB=-L$(DPMTADIR) -ldpmta
#PMTAFLAGS=-DDPMTA
#DPMTA=$(PMTAINCL) $(PMTAFLAGS)
d37 3
a39 2
#PVMDIR=/usr/local/shared/pvm/pvm3/lib/HPPA
#PVMLIB=-L$(PVMDIR) -lpvm3
d46 1
a46 1
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(CXXOPTS) $(NOWARN)
d130 2
a131 1
	cd $(DPMTADIR) ; $(MAKE) libdpmta.a ; cd ..
d136 3
a138 2
	$(PMTALIB) \
	$(PVMLIB)
@


1.1005
log
@Intermediate debuging commit - working to fix deep bug in migration"?
@
text
@d31 1
a31 2
#PMTALIBDIR=-L$(DPMTADIR)
#PMTALIB=-ldpmta
d38 1
a38 2
#PVMLIBDIR=-L$(PVMDIR)
#PVMLIB=-lpvm3
d134 2
a135 2
	$(PMTALIBDIR) $(PMTALIB) \
	$(PVMLIBDIR) $(PVMLIB)
@


1.1004
log
@Added dcd file objects.
@
text
@d13 8
d23 2
a24 2
CHARMC = /Projects/l1/namd.2.0/charm/bin/charmc
CHARMXI = /Projects/l1/namd.2.0/charm/bin/charmc
d30 11
a40 11
PMTAINCL=-I$(DPMTADIR)
PMTALIBDIR=-L$(DPMTADIR)
PMTALIB=-ldpmta
PMTAFLAGS=-DDPMTA
DPMTA=$(PMTAINCL) $(PMTAFLAGS)
#####
# definitions for PVM routines
#####
PVMDIR=/usr/local/shared/pvm/pvm3/lib/HPPA
PVMLIBDIR=-L$(PVMDIR)
PVMLIB=-lpvm3
d47 2
a48 2
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(CXXOPTS) -w
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) -w
@


1.1003
log
@Ari - attempting to get makefile committed
@
text
@d51 1
d91 1
@


1.1002
log
@Now includes DPMTA directory.
@
text
@d120 2
a121 1
namd2:	$(DPMTALIB) $(INCDIR) $(DSTDIR) $(OBJS) $(TEMPLATES)
a159 5


obj/libdpmta.a:
	cd $(DPMTADIR) ; $(MAKE) libdpmta.a ; cd ..
	$(COPY) $(DPMTADIR)/libdpmta.a ../$(DSTDIR)
@


1.1001
log
@Minor tweek for compiling - left out DPMTA also
@
text
@d3 10
d21 6
a26 6
#PMTADIR=/Projects/l2/namd/dpmta-2.5/src
#PMTAINCL=-I$(PMTADIR)
#PMTALIBDIR=-L$(PMTADIR)
#PMTALIB=-ldpmta
#PMTAFLAGS=-DDPMTA
#DPMTA=$(PMTAINCL) $(PMTAFLAGS)
d30 3
a32 13
#PVMDIR=/usr/local/shared/pvm/pvm3/lib/HPPA
#PVMLIBDIR=-L$(PVMDIR)
#PVMLIB=-lpvm3

#####
# Directories
#####
# source directory
SRCDIR = src
# destination directory (binaries) -- currently, MUST be .
DSTDIR = obj
# temp include directory for cifiles
INCDIR = inc
d47 1
d120 1
a120 1
namd2:	$(INCDIR) $(DSTDIR) $(OBJS) $(TEMPLATES)
d160 5
d183 1
@


1.1000
log
@Resetting CVS to merge branches back into the main trunk.
We will stick to main trunk development as suggested by CVS manual.
We will set up tags to track fixed points of development/release
as suggested by CVS manual - all praise the CVS manual.
@
text
@d11 6
a16 6
PMTADIR=/Projects/l2/namd/dpmta-2.5/src
PMTAINCL=-I$(PMTADIR)
PMTALIBDIR=-L$(PMTADIR)
PMTALIB=-ldpmta
PMTAFLAGS=-DDPMTA
DPMTA=$(PMTAINCL) $(PMTAFLAGS)
d20 3
a22 3
PVMDIR=/usr/local/shared/pvm/pvm3/lib/HPPA
PVMLIBDIR=-L$(PVMDIR)
PVMLIB=-lpvm3
@


1.779
log
@Updating Revision Line, getting rid of branches
@
text
@@


1.778
log
@internal release uplevel to 1.778
@
text
@d1 4
d8 19
d34 2
a35 1
CXXOPTS = -O
d39 2
a40 2
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(CXXOPTS)  -w
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) -w
d62 1
d108 18
a125 2
namd2:	$(INCDIR) $(DSTDIR) $(OBJS)
	$(CHARMC) -ld++-option "-I $(INCLUDE) -I $(SRCDIR) $(CXXOPTS)" -language charm++ -o namd2 $(OBJS)
@


1.778.2.1
log
@Added migration code
@
text
@d11 1
a11 1
CXXOPTS = -g
@


1.778.2.2
log
@Added explicit dependencies for templates.
@
text
@d83 1
a83 12
TEMPLATES = \
	$(SRCDIR)/ComputeHomeTuples.C \
	$(SRCDIR)/PositionBox.C \
	$(SRCDIR)/PositionOwnerBox.C \
	$(SRCDIR)/Templates/Box.C \
	$(SRCDIR)/Templates/OwnerBox.C \
	$(SRCDIR)/Templates/ResizeArray.C \
	$(SRCDIR)/Templates/SortableResizeArray.C \
	$(SRCDIR)/Templates/SortedArray.C \
	$(SRCDIR)/Templates/UniqueSortedArray.C

namd2:	$(INCDIR) $(DSTDIR) $(OBJS) $(TEMPLATES)
@


1.778.2.3
log
@Added ComputeFullDirect.
@
text
@a37 1
	$(DSTDIR)/ComputeFullDirect.o \
@


1.778.2.4
log
@Added PVM and DPMTA
@
text
@a0 4

#####
# definitions for Charm routines
#####
a3 19
#####
# definitions for PMTA routines
#####
PMTADIR=/Projects/l2/namd/dpmta-2.5/src
PMTAINCL=-I$(PMTADIR)
PMTALIBDIR=-L$(PMTADIR)
PMTALIB=-ldpmta
PMTAFLAGS=-DDPMTA
DPMTA=$(PMTAINCL) $(PMTAFLAGS)
#####
# definitions for PVM routines
#####
PVMDIR=/usr/local/shared/pvm/pvm3/lib/HPPA
PVMLIBDIR=-L$(PVMDIR)
PVMLIB=-lpvm3

#####
# Directories
#####
a10 1
# CXXOPTS = -O
d15 2
a16 2
CXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) $(CXXOPTS) -w
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) $(DPMTA) -w
d96 1
a96 6
	$(CHARMC) -ld++-option \
	"-I $(INCLUDE) -I $(SRCDIR) $(CXXOPTS) " \
	-language charm++ \
	-o namd2 $(OBJS) \
	$(PMTALIBDIR) $(PMTALIB) \
	$(PVMLIBDIR) $(PVMLIB)
@


1.777
log
@Internal CVS leveling release.  Start development code work
at 1.777.1.1.
@
text
@d7 1
a7 1
DSTDIR = .
d11 2
a12 1
CXXOPTS = -g
d16 1
d25 53
a77 29
	main.o \
	AtomMap.o \
	common.o strlib.o \
	CollectionMaster.o CollectionMgr.o \
	Communicate.o CommunicateConverse.o \
	Compute.o \
	ComputeAngles.o ComputeBonds.o ComputeDihedrals.o ComputeImpropers.o \
	ComputeGeneral.o ComputeMap.o ComputeMgr.o \
	ComputeNonbondedExcl.o ComputeNonbondedSelf.o \
	ComputeNonbondedPair.o ComputeNonbondedUtil.o \
	ComputePatch.o ComputePatchPair.o \
	ConfigList.o \
	Controller.o \
	HomePatch.o \
	Inform.o InfoStream.o IntTree.o \
	LJTable.o \
	Message.o MessageManager.o MessageQueue.o \
	Molecule.o \
	Namd.o NamdState.o \
	Node.o \
	ParseOptions.o Parameters.o \
	SimParameters.o PDB.o PDBData.o \
	Patch.o PatchMgr.o PatchMap.o \
	ProxyMgr.o ProxyPatch.o \
	ReductionMgr.o \
	Sequencer.o \
	WorkDistrib.o

CXXFILES = $(OBJS:.o=.C)
d84 1
a84 1
	$(CHARMC) -ld++-option "-I $(INCLUDE) -I $(SRCDIR)" -g -language charm++ -o namd2 $(OBJS)
d93 4
a96 1
depends: $(DEPENDSFILE)
d102 9
a110 6
	for i in ZZZ $(CXXFILES) ; do \
	   if [ "$$i" != "ZZZ" -a -f $(SRCDIR)/$$i ]; then \
	      $(ECHO) "checking dependencies for $$i ..."; \
	      g++ -MM $(CXXFLAGS) $(SRCDIR)/$$i |  \
	      $(SRCDIR)/dc.pl $(INCLUDE) /usr/include >> $(DEPENDFILE);\
	   fi; \
a132 1
	rm -f *.o
d134 2
d138 4
a141 1
	rm -f $(INCDIR)/*.top.h $(INCDIR)/*.bot.h *.depends
@


1.777.2.1
log
@Makefile updated to use obj/ directory for .o files.
@
text
@d7 1
a7 1
DSTDIR = obj
d23 27
a49 49
	$(DSTDIR)/common.o \
	$(DSTDIR)/main.o \
	$(DSTDIR)/strlib.o \
	$(DSTDIR)/AtomMap.o \
	$(DSTDIR)/CollectionMaster.o \
	$(DSTDIR)/CollectionMgr.o \
	$(DSTDIR)/Communicate.o \
	$(DSTDIR)/CommunicateConverse.o \
	$(DSTDIR)/Compute.o \
	$(DSTDIR)/ComputeAngles.o \
	$(DSTDIR)/ComputeBonds.o \
	$(DSTDIR)/ComputeDihedrals.o \
	$(DSTDIR)/ComputeImpropers.o \
	$(DSTDIR)/ComputeGeneral.o \
	$(DSTDIR)/ComputeMap.o \
	$(DSTDIR)/ComputeMgr.o \
	$(DSTDIR)/ComputeNonbondedExcl.o \
	$(DSTDIR)/ComputeNonbondedSelf.o \
	$(DSTDIR)/ComputeNonbondedPair.o \
	$(DSTDIR)/ComputeNonbondedUtil.o \
	$(DSTDIR)/ComputePatch.o \
	$(DSTDIR)/ComputePatchPair.o \
	$(DSTDIR)/ConfigList.o \
	$(DSTDIR)/Controller.o \
	$(DSTDIR)/HomePatch.o \
	$(DSTDIR)/Inform.o \
	$(DSTDIR)/InfoStream.o \
	$(DSTDIR)/IntTree.o \
	$(DSTDIR)/LJTable.o \
	$(DSTDIR)/Message.o \
	$(DSTDIR)/MessageManager.o \
	$(DSTDIR)/MessageQueue.o \
	$(DSTDIR)/Molecule.o \
	$(DSTDIR)/Namd.o \
	$(DSTDIR)/NamdState.o \
	$(DSTDIR)/Node.o \
	$(DSTDIR)/Parameters.o \
	$(DSTDIR)/ParseOptions.o \
	$(DSTDIR)/Patch.o \
	$(DSTDIR)/PatchMgr.o \
	$(DSTDIR)/PatchMap.o \
	$(DSTDIR)/PDB.o \
	$(DSTDIR)/PDBData.o \
	$(DSTDIR)/ProxyMgr.o \
	$(DSTDIR)/ProxyPatch.o \
	$(DSTDIR)/ReductionMgr.o \
	$(DSTDIR)/Sequencer.o \
	$(DSTDIR)/SimParameters.o \
	$(DSTDIR)/WorkDistrib.o
d67 1
a67 4
# make depends is ugly!  The problem: we have obj/file.o and want src/file.C.
# Solution: heavy use of basename and awk.
# This is a CPU killer...  Don't make depends if you don't need to.
depends: $(DSTDIR) $(DEPENDSFILE)
d73 6
a78 9
	for i in $(OBJS) ; do \
	      $(ECHO) "checking dependencies for" \
	        `basename $$i | awk -F. '{print $$1".C"}'` ; \
	      g++ -MM $(CXXFLAGS) \
	        $(SRCDIR)/`basename $$i | awk -F. '{print $$1".C"}'` | \
	      $(SRCDIR)/dc.pl $(INCLUDE) /usr/include >> $(DEPENDFILE); \
	      $(ECHO) "\t$$(CXX) $$(CXXFLAGS) -o "$$i" -c" \
	        "$$(SRCDIR)/"`basename $$i | awk -F. '{print $$1".C"}'` \
		>> $(DEPENDFILE) ; \
@


1.777.2.2
log
@Modified "make clean" to support the obj and inc directories.
@
text
@d92 1
a92 1
depends: cifiles $(DSTDIR) $(DEPENDSFILE)
d129 1
a130 2
	rm -rf $(DSTDIR)
	rm -f namd2
d133 1
a133 4
	rm -rf $(INCDIR)
	rm -f *.depends
	# allow for the makefile to continue to work
	touch Make.depends
@


1.777.2.3
log
@One final change in "make veryclean" -- the touch now uses $(DEPENDFILE).
@
text
@d137 1
a137 1
	touch $(DEPENDFILE)
@


1.777.2.4
log
@Removed CXXFILES -- unused.
@
text
@d73 2
@


1.777.2.5
log
@switched -g to -O
@
text
@d11 1
a11 1
CXXOPTS = -O
d78 1
a78 1
	$(CHARMC) -ld++-option "-I $(INCLUDE) -I $(SRCDIR)" $(CXXOPTS) -language charm++ -o namd2 $(OBJS)
@


1.777.2.6
log
@Cleaned up depends to allow for compiling for K-boxes.
@
text
@a11 1
# CXXOPTS = -O +DAK460 +DSK460
a14 1
GXXFLAGS = -I$(INCLUDE) -I$(SRCDIR) -I$(INCDIR) -w
d78 1
a78 1
	$(CHARMC) -ld++-option "-I $(INCLUDE) -I $(SRCDIR) $(CXXOPTS)" -language charm++ -o namd2 $(OBJS)
d99 1
a99 1
	      g++ -MM $(GXXFLAGS) \
d101 1
a101 1
	      $(SRCDIR)/dc.pl $(INCLUDE) /usr/include /usr/local >> $(DEPENDFILE); \
@


1.777.2.7
log
@Added files for hydrogen bond parameter reading.
@
text
@a49 1
	$(DSTDIR)/HBondParam.o \
a72 1
	$(DSTDIR)/VoidTree.o \
@


1.777.2.8
log
@*** empty log message ***
@
text
@a36 2
	$(DSTDIR)/ComputeDPMTA.o \
	$(DSTDIR)/ComputeHomePatches.o \
@


1.31
log
@Changed make clean and veryclean.  (Minor changing).
@
text
@@


1.30
log
@Modified Makefile and dc.pl to work with CVS.  In particular, the
src directory is never touched during compilation.
@
text
@a101 1
	rm -f $(SRCDIR)/*.o
d104 1
a104 3
veryclean:
	rm -f *.o
	rm -rf ptrepository
@


1.29
log
@added Collection files
@
text
@d4 7
d14 1
a14 1
CXXFLAGS = -I$(INCLUDE) $(CXXOPTS)  -w
d23 27
a49 13
	main.o Message.o Molecule.o PDB.o PDBData.o \
	ConfigList.o Inform.o InfoStream.o Parameters.o common.o \
	strlib.o SimParameters.o ParseOptions.o Namd.o \
	NamdState.o WorkDistrib.o Node.o PatchMap.o ComputeMap.o \
	PatchMgr.o Patch.o HomePatch.o Sequencer.o Compute.o \
	ComputeGeneral.o AtomMap.o ComputePatchPair.o \
	ComputePatch.o ComputeNonbondedUtil.o LJTable.o \
	ComputeNonbondedSelf.o ComputeNonbondedPair.o \
	ComputeAngles.o ComputeDihedrals.o ComputeImpropers.o \
	ComputeBonds.o ComputeNonbondedExcl.o ComputeMgr.o \
	ProxyMgr.o ProxyPatch.o CommunicateConverse.o \
	Communicate.o IntTree.o MessageQueue.o MessageManager.o \
	ReductionMgr.o Controller.o CollectionMgr.o CollectionMaster.o
d57 2
a58 2
namd2:	$(OBJS)
	$(CHARMC) -ld++-option "-I $(INCLUDE)" -g -language charm++ -o namd2 $(OBJS)
d60 1
a60 1
cifiles:
d62 1
a62 1
	   $(CHARMXI) $$i; \
d64 2
d74 1
a74 1
	   if [ "$$i" != "ZZZ" -a -f $$i ]; then \
d76 2
a77 2
	      g++ -MM $(CXXFLAGS) $$i |  \
	      dc.pl $(INCLUDE) /usr/include >> $(DEPENDFILE);\
d86 1
a86 1
$(INTERFACES:.ci=.top.h):	$$(@@:.top.h=.ci)
d88 1
d90 1
a90 1
$(INTERFACES:.ci=.bot.h):	$$(@@:.bot.h=.ci)
d92 4
d97 2
d102 1
d108 2
a109 1
	rm -f *.top.h *.bot.h *.depends
@


1.28
log
@added Controller.o
@
text
@d28 1
a28 1
	ReductionMgr.o Controller.o
d33 2
a34 1
		ComputeMgr.ci ProxyMgr.ci ReductionMgr.ci
@


1.27
log
@Added ReductionMgr.ci.
@
text
@d28 1
a28 1
	ReductionMgr.o
@


1.26
log
@Added ReductionMgr.o
@
text
@d33 1
a33 1
		ComputeMgr.ci ProxyMgr.ci
@


1.25
log
@added CommunicateConverse material
@
text
@d27 2
a28 1
	Communicate.o IntTree.o MessageQueue.o MessageManager.o
@


1.24
log
@*** empty log message ***
@
text
@d26 2
a27 1
	ProxyMgr.o ProxyPatch.o
@


1.23
log
@*** empty log message ***
@
text
@d26 1
a26 1
	ProxyMgr.o
@


1.22
log
@Added ComputeNonbondedExcl.o
@
text
@d25 2
a26 1
	ComputeBonds.o ComputeNonbondedExcl.o ComputeMgr.o
d30 2
a31 1
INTERFACES = main.ci Node.ci WorkDistrib.ci PatchMgr.ci Compute.ci ComputeMgr.ci
@


1.21
log
@Added ComputeBonds.
@
text
@d25 1
a25 1
	ComputeBonds.o ComputeMgr.o
@


1.20
log
@added ComputeMgr and some Computes
@
text
@d25 1
a25 1
	ComputeMgr.o
@


1.19
log
@*** empty log message ***
@
text
@d24 2
a25 1
	ComputeAngles.o
d29 1
a29 1
INTERFACES = main.ci Node.ci WorkDistrib.ci PatchMgr.ci Compute.ci
@


1.18
log
@added fix for Make.depends
@
text
@d4 1
d7 1
a7 1
CXXFLAGS = -I$(INCLUDE) $(CXXOPTS) -w
@


1.17
log
@Added InfoStream.o to objects list.
@
text
@d46 2
a47 2
	      g++ -MM $(CXXFLAGS) $$i |grep -v "/usr/include" \
	      | grep -v \"$(INCLUDE)\" >> $(DEPENDFILE);\
@


1.16
log
@*** empty log message ***
@
text
@d16 1
a16 1
	ConfigList.o Inform.o Parameters.o common.o \
d46 2
a47 1
	      g++ -MM $(CXXFLAGS) $$i |grep -v "/usr/include" >> $(DEPENDFILE);\
@


1.15
log
@added files for Nonbonded computation
@
text
@d22 2
a23 1
	ComputeNonbondedSelf.o ComputeNonbondedPair.o
@


1.14
log
@Added AtomMap
@
text
@d20 3
a22 1
	ComputeGeneral.o AtomMap.o
@


1.13
log
@*** empty log message ***
@
text
@d20 1
a20 1
	ComputeGeneral.o
@


1.12
log
@*** empty log message ***
@
text
@d19 2
a20 1
	PatchMgr.o Patch.o HomePatch.o Sequencer.o Compute.o
@


1.11
log
@Added Sequencer.o to list.
@
text
@d19 1
a19 1
	PatchMgr.o Patch.o HomePatch.o Sequencer.o
d23 1
a23 1
INTERFACES = main.ci Node.ci WorkDistrib.ci PatchMgr.ci
@


1.10
log
@*** empty log message ***
@
text
@d19 1
a19 1
	PatchMgr.o Patch.o HomePatch.o
@


1.9
log
@*** empty log message ***
@
text
@d6 1
a6 1
CXXFLAGS = -I$(INCLUDE) $(CXXOPTS)
d59 2
a60 1
	rm -rf *.o
d63 2
a64 1
	rm -rf *.o
@


1.8
log
@*** empty log message ***
@
text
@d33 1
a33 1
depends: 
d45 3
@


1.7
log
@*** empty log message ***
@
text
@d5 2
a6 1
CXXFLAGS = -I/Projects/l1/namd.2.0/charm/include $(CXXOPTS)
d18 2
a19 1
	NamdState.o WorkDistrib.o Node.o PatchMap.o ComputeMap.o
d23 1
a23 1
INTERFACES = main.ci Node.ci WorkDistrib.ci
d26 1
a26 1
	$(CHARMC) -g -language charm++ -o namd2 $(OBJS)
@


1.6
log
@*** empty log message ***
@
text
@d55 3
@


1.5
log
@*** empty log message ***
@
text
@d55 1
@


1.4
log
@*** empty log message ***
@
text
@d17 1
a17 1
	NamdState.o
d21 1
a21 1
INTERFACES = main.ci
@


1.3
log
@*** empty log message ***
@
text
@d4 2
a5 2
CXX = CC -Aa -D_HPUX_SOURCE -g
CXXFLAGS = -I/Projects/l1/namd.2.0/charm/include
d14 4
a17 1
	main.o Message.o Molecule.o PDB.o PDBData.o ConfigList.o Inform.o Parameters.o common.o strlib.o SimParameters.o ParseOptions.o
@


1.2
log
@*** empty log message ***
@
text
@d4 1
a4 1
CXX = g++
d21 1
a21 1
	$(CHARMC) -language charm++ -o namd2 $(OBJS)
@


1.1
log
@Initial revision
@
text
@d1 2
a2 2
CHARMC = /Projects/l1/namd.2.0/charm/net-hp/bin/charmc
CHARMXI = /Projects/l1/namd.2.0/charm/net-hp/bin/charmxi
d5 1
a5 1
CXXFLAGS = -I/Projects/l1/namd.2.0/charm/net-hp/include
d14 1
a14 1
	main.o
d28 1
a28 1
depends:
d49 3
@
