| Time | Author | Lines | Revision | Filename | Comments |
| 2017/05/16 21:14:26 | jim | +75 -6 | 1.34 | ug/ug_colvars.tex | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +48 -20 | 1.17 | src/colvarvalue.h | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +2 -2 | 1.12 | src/colvarvalue.C | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +5 -0 | 1.17 | src/colvartypes.h | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +1 -1 | 1.7 | src/colvarscript.h | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +2 -5 | 1.11 | src/colvarscript.C | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +1 -3 | 1.2 | src/colvars_version.h | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +2 -2 | 1.29 | src/colvarproxy_namd.C | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +11 -2 | 1.30 | src/colvarmodule.h | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +52 -21 | 1.32 | src/colvarmodule.C | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +1 -1 | 1.19 | src/colvargrid.h | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +79 -28 | 1.5 | src/colvardeps.h | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +207 -39 | 1.7 | src/colvardeps.C | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +14 -6 | 1.21 | src/colvarcomp_distances.C | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +145 -0 | 1.17 | src/colvarcomp_angles.C | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +67 -2 | 1.26 | src/colvarcomp.h | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +106 -91 | 1.14 | src/colvarcomp.C | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +7 -6 | 1.8 | src/colvarbias_restraint.C | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +10 -8 | 1.24 | src/colvarbias_abf.C | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +1 -1 | 1.17 | src/colvarbias.h | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +15 -5 | 1.20 | src/colvarbias.C | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +8 -4 | 1.17 | src/colvaratoms.h | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +99 -24 | 1.27 | src/colvaratoms.C | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +8 -14 | 1.19 | src/colvar.h | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/05/16 21:14:20 | jim | +66 -45 | 1.35 | src/colvar.C | Update Colvars to fd7445328d5f670863690869bf95716dce8a1dd8 |
| 2017/04/30 17:20:56 | jim | +1 -1 | 1.8 | arch/Linux-x86_64-g++.arch | Change c++11 to c++0x to work with gcc 4.4. |
| 2017/04/30 17:20:56 | jim | +1 -1 | 1.4 | arch/Linux-x86-g++.arch | Change c++11 to c++0x to work with gcc 4.4. |
| 2017/04/28 15:32:40 | dhardy | +1 -1 | 1.7 | arch/Linux-x86_64-g++.arch | Use of auto typing in ComputeQM.C needs -std=c++11 compile option to g++ |
| 2017/04/28 15:32:40 | dhardy | +1 -1 | 1.3 | arch/Linux-x86-g++.arch | Use of auto typing in ComputeQM.C needs -std=c++11 compile option to g++ |
| 2017/04/21 21:15:13 | dhardy | +6 -0 | 1.1159 | src/Node.C | Split MSM initialization into two phases to avoid race conditions.Phase 1 initializes the overall Map object that, in part, indicatesthe PE for each chare. Phase 2 creates the chares. |
| 2017/04/21 21:15:13 | dhardy | +1 -0 | 1.21 | src/ComputeMsmMgr.ci | Split MSM initialization into two phases to avoid race conditions.Phase 1 initializes the overall Map object that, in part, indicatesthe PE for each chare. Phase 2 creates the chares. |
| 2017/04/21 21:15:13 | dhardy | +18 -2 | 1.73 | src/ComputeMsm.C | Split MSM initialization into two phases to avoid race conditions.Phase 1 initializes the overall Map object that, in part, indicatesthe PE for each chare. Phase 2 creates the chares. |
| 2017/04/12 16:15:08 | dhardy | +33 -33 | 1.1158 | src/Node.C | Rearranged startup order so that MSM is started BEFORE CUDA.This seems to fix the bug that Jim found where MSM startupfor tutorial (non-periodic sphere) crashes when using a CUDAdevice with multiple CPU cores. |
| 2017/04/02 18:33:13 | jim | +24 -9 | 1.1266 | src/Molecule.C | Speed up dihedral parameter assignment when reading from js file. |
| 2017/04/01 19:43:04 | jim | +3 -1 | 1.80 | src/BackEnd.C | Suspend to finish creating groups, allowing use of CkLoop during startup. |
| 2017/04/01 19:15:01 | jim | +8 -8 | 1.121 | notes.txt | Update to Charm++ 6.8.0-beta1. |
| 2017/04/01 19:15:01 | jim | +1 -1 | 1.112 | config | Update to Charm++ 6.8.0-beta1. |
| 2017/04/01 19:15:01 | jim | +2 -2 | 1.35 | Make.charm | Update to Charm++ 6.8.0-beta1. |
| 2017/03/31 18:16:03 | jim | +20 -3 | 1.1058 | src/Parameters.C | Only modify dihedral/improper multiplicity from psf for ancient X-PLOR parameters. |
| 2017/03/30 20:06:17 | jim | +10 -2 | 1.1291 | src/WorkDistrib.C | 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. |
| 2017/03/30 20:06:17 | jim | None | 1.1 | src/TupleTypesCUDA.h | 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. |
| 2017/03/30 20:06:17 | jim | +3 -2 | 1.1248 | src/SimParameters.h | 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. |
| 2017/03/30 20:06:17 | jim | +20 -17 | 1.1478 | src/SimParameters.C | 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. |
| 2017/03/30 20:06:17 | jim | +2 -0 | 1.1114 | src/ProxyMgr.C | 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. |
| 2017/03/30 20:06:17 | jim | +1 -1 | 1.1157 | src/Node.C | 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. |
| 2017/03/30 20:06:17 | jim | +4 -4 | 1.40 | src/NamdHybridLB.C | 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. |
| 2017/03/30 20:06:17 | jim | +4 -4 | 1.125 | src/NamdCentLB.C | 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. |
| 2017/03/30 20:06:17 | jim | +57 -23 | 1.128 | src/LdbCoordinator.C | 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. |
| 2017/03/30 20:06:17 | jim | +15 -0 | 1.1036 | src/Lattice.h | 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. |
| 2017/03/30 20:06:17 | jim | +0 -4 | 1.5 | src/DeviceCUDA.h | 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. |
| 2017/03/30 20:06:17 | jim | +0 -6 | 1.6 | src/DeviceCUDA.C | 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. |
| 2017/03/30 20:06:17 | jim | +0 -4 | 1.4 | src/CudaUtils.h | 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. |
| 2017/03/30 20:06:17 | jim | +1 -1 | 1.2 | src/CudaTileListKernel.h | 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. |
| 2017/03/30 20:06:17 | jim | +7 -6 | 1.3 | src/CudaTileListKernel.cu | 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. |
| 2017/03/30 20:06:17 | jim | +10 -20 | 1.2 | src/CudaPmeSolverUtilKernel.h | 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. |
| 2017/03/30 20:06:17 | jim | +155 -749 | 1.2 | src/CudaPmeSolverUtilKernel.cu | 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. |
| 2017/03/30 20:06:17 | jim | +3 -6 | 1.2 | src/CudaPmeSolverUtil.h | 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. |
| 2017/03/30 20:06:17 | jim | +65 -116 | 1.3 | src/CudaPmeSolverUtil.C | 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. |
| 2017/03/30 20:06:17 | jim | +2 -6 | 1.2 | src/CudaPmeSolver.C | 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. |
| 2017/03/30 20:06:17 | jim | None | 1.1 | src/CudaNonbondedTables.h | 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. |
| 2017/03/30 20:06:17 | jim | None | 1.1 | src/CudaNonbondedTables.C | 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. |
| 2017/03/30 20:06:17 | jim | +4 -35 | 1.2 | src/CudaComputeNonbondedKernel.h | 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. |
| 2017/03/30 20:06:17 | jim | +16 -197 | 1.2 | src/CudaComputeNonbondedKernel.cu | 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. |
| 2017/03/30 20:06:17 | jim | +4 -6 | 1.2 | src/CudaComputeNonbonded.h | 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. |
| 2017/03/30 20:06:17 | jim | +177 -178 | 1.3 | src/CudaComputeNonbonded.C | 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. |
| 2017/03/30 20:06:17 | jim | +3 -3 | 1.2 | src/CudaComputeGBISKernel.h | 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. |
| 2017/03/30 20:06:17 | jim | +10 -10 | 1.2 | src/CudaComputeGBISKernel.cu | 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. |
| 2017/03/30 20:06:17 | jim | +138 -2 | 1.27 | src/ComputeSelfTuples.h | 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. |
| 2017/03/30 20:06:17 | jim | +1 -1 | 1.3 | src/ComputePmeCUDAMgr.h | 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. |
| 2017/03/30 20:06:17 | jim | +0 -1 | 1.2 | src/ComputePmeCUDAMgr.C | 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. |
| 2017/03/30 20:06:17 | jim | +67 -23 | 1.2 | src/ComputePmeCUDA.C | 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. |
| 2017/03/30 20:06:17 | jim | +1 -0 | 1.1094 | src/ComputeNonbondedUtil.h | 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. |
| 2017/03/30 20:06:17 | jim | +2 -0 | 1.1126 | src/ComputeNonbondedUtil.C | 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. |
| 2017/03/30 20:06:17 | jim | +21 -0 | 1.1047 | src/ComputeMgr.h | 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. |
| 2017/03/30 20:06:17 | jim | +13 -0 | 1.1024 | src/ComputeMgr.ci | 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. |
| 2017/03/30 20:06:17 | jim | +369 -40 | 1.1133 | src/ComputeMgr.C | 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. |
| 2017/03/30 20:06:17 | jim | +3 -0 | 1.1060 | src/ComputeMap.h | 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. |
| 2017/03/30 20:06:17 | jim | +240 -2 | 1.1065 | src/ComputeHomeTuples.h | 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. |
| 2017/03/30 20:06:17 | jim | +12 -0 | 1.2 | src/ComputeCUDAMgr.h | 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. |
| 2017/03/30 20:06:17 | jim | +45 -2 | 1.2 | src/ComputeCUDAMgr.C | 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. |
| 2017/03/30 20:06:17 | jim | None | 1.1 | src/ComputeBondedCUDAKernel.h | 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. |
| 2017/03/30 20:06:17 | jim | None | 1.1 | src/ComputeBondedCUDAKernel.cu | 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. |
| 2017/03/30 20:06:17 | jim | None | 1.1 | src/ComputeBondedCUDA.h | 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. |
| 2017/03/30 20:06:17 | jim | None | 1.1 | src/ComputeBondedCUDA.C | 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. |
| 2017/03/30 20:06:17 | jim | +10 -0 | 1.1018 | src/AtomMap.h | 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. |
| 2017/03/30 20:06:13 | jim | +6 -4 | 1.1361 | Makefile | 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. |
| 2017/03/30 20:06:13 | jim | +197 -14 | 1.199 | Make.depends | 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. |
| 2017/03/30 19:53:15 | jim | +4 -4 | 1.7 | plugins/molfile_plugin/src/jsplugin.c | Disable block-based I/O since psfgen does not align coordinate buffer properly. |
| 2017/03/30 16:09:59 | jim | +3 -0 | 1.1020 | src/InfoStream.C | Fix int64 output on Mac. |
| 2017/03/30 16:02:54 | jim | +3 -0 | 1.1021 | src/InfoStream.h | Fix int64 output on Mac. |
| 2017/03/29 21:38:53 | jim | +4 -4 | 1.4 | plugins/molfile_plugin/src/readpdb.h | Update from VMD plugins tree (copyright notice only). |
| 2017/03/29 21:38:53 | jim | +4 -4 | 1.10 | plugins/molfile_plugin/src/psfplugin.c | Update from VMD plugins tree (copyright notice only). |
| 2017/03/29 21:38:53 | jim | +4 -4 | 1.4 | plugins/molfile_plugin/src/pdbplugin.c | Update from VMD plugins tree (copyright notice only). |
| 2017/03/29 21:38:53 | jim | +1 -1 | 1.4 | plugins/molfile_plugin/src/namdbinplugin.c | Update from VMD plugins tree (copyright notice only). |
| 2017/03/29 21:38:53 | jim | +4 -4 | 1.5 | plugins/molfile_plugin/src/largefiles.h | Update from VMD plugins tree (copyright notice only). |
| 2017/03/29 21:38:53 | jim | +1 -1 | 1.5 | plugins/molfile_plugin/src/hash.h | Update from VMD plugins tree (copyright notice only). |
| 2017/03/29 21:38:53 | jim | +1 -1 | 1.5 | plugins/molfile_plugin/src/hash.c | Update from VMD plugins tree (copyright notice only). |
| 2017/03/29 21:38:53 | jim | +4 -4 | 1.4 | plugins/molfile_plugin/src/fortread.h | Update from VMD plugins tree (copyright notice only). |
| 2017/03/29 21:38:53 | jim | +4 -4 | 1.6 | plugins/molfile_plugin/src/endianswap.h | Update from VMD plugins tree (copyright notice only). |
| 2017/03/29 21:38:53 | jim | +1 -1 | 1.8 | plugins/molfile_plugin/src/dcdplugin.c | Update from VMD plugins tree (copyright notice only). |
| 2017/03/29 21:38:15 | jim | +72 -41 | 1.6 | plugins/molfile_plugin/src/jsplugin.c | Update from VMD plugins tree. |
| 2017/03/29 21:38:15 | jim | +16 -6 | 1.9 | plugins/molfile_plugin/src/fastio.h | Update from VMD plugins tree. |
| 2017/03/29 21:29:04 | jim | +2 -2 | 1.1092 | src/NamdState.C | Minimal change for testing billion-atom systems. |
| 2017/03/29 21:29:03 | jim | +6 -6 | 1.1121 | src/Molecule.h | Minimal change for testing billion-atom systems. |
| 2017/03/29 21:29:03 | jim | +1 -1 | 1.1093 | src/Controller.h | Minimal change for testing billion-atom systems. |
| 2017/03/29 21:29:03 | jim | +3 -3 | 1.1326 | src/Controller.C | Minimal change for testing billion-atom systems. |
| 2017/03/29 21:10:44 | jim | +16 -13 | 1.13 | psfgen/src/topo_mol_pluginio.c | Minimal change to allow writing tiled billion-atom systems for testing. |
| 2017/03/29 19:25:55 | dhardy | +1 -0 | 1.72 | src/ComputeMsm.C | Added another comment |
| 2017/03/29 19:03:04 | dhardy | +2 -0 | 1.71 | src/ComputeMsm.C | Added comment to test mail from CVS check-in |
| 2017/03/29 15:06:40 | jim | +2 -2 | 1.37 | psfgen/src/tcl_psfgen.c | Support 2 GB hasharrays to enable 2^25 residues per segment, increase version to 1.6.7. |
| 2017/03/29 15:06:40 | jim | +1 -1 | 1.3 | psfgen/src/hasharray.c | Support 2 GB hasharrays to enable 2^25 residues per segment, increase version to 1.6.7. |
| 2017/03/28 19:45:55 | jim | +2 -1 | 1.1156 | src/Node.C | Only call ckNew() on pe 0. |
| 2017/03/28 19:45:55 | jim | +2 -2 | 1.2 | src/ComputePmeCUDAMgr.ci | Only call ckNew() on pe 0. |
| 2017/03/28 19:45:52 | jim | +8 -0 | 1.198 | Make.depends | Only call ckNew() on pe 0. |
| 2017/03/24 18:08:24 | dhardy | +2 -2 | 1.1155 | src/Node.C | Fixed bug: MSM not getting initialized whenever CUDA2 is active |
| 2017/03/22 22:06:33 | jim | +3 -1 | 1.1360 | Makefile | Build NAMD .c files with $(CC) instead of $(CXX), but still use $(CXXFLAGS) |
| 2017/03/22 22:06:33 | jim | +7 -7 | 1.197 | Make.depends | Build NAMD .c files with $(CC) instead of $(CXX), but still use $(CXXFLAGS) |
| 2017/03/21 20:18:42 | jim | +26 -0 | 1.196 | Make.depends | Rebuild after Colvars update. |
| 2017/03/21 20:17:09 | jim | None | 1.1 | src/colvars_version.h | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:17:09 | jim | None | 1.1 | src/colvarproxy_namd_version.h | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +4 -272 | 1.16 | src/colvarvalue.h | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +275 -0 | 1.11 | src/colvarvalue.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +13 -5 | 1.6 | src/colvarscript.h | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +71 -68 | 1.10 | src/colvarscript.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +14 -4 | 1.17 | src/colvarproxy_namd.h | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +10 -0 | 1.28 | src/colvarproxy_namd.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +5 -0 | 1.18 | src/colvarproxy.h | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +4 -21 | 1.11 | src/colvarparse.h | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +26 -27 | 1.13 | src/colvarparse.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +1 -3 | 1.29 | src/colvarmodule.h | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +4 -2 | 1.31 | src/colvarmodule.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +0 -4 | 1.18 | src/colvargrid.h | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +39 -24 | 1.4 | src/colvardeps.h | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +112 -96 | 1.6 | src/colvardeps.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +2 -2 | 1.15 | src/colvarcomp_protein.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +10 -10 | 1.20 | src/colvarcomp_distances.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +4 -4 | 1.16 | src/colvarcomp_angles.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +22 -11 | 1.13 | src/colvarcomp.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +0 -1 | 1.7 | src/colvarbias_restraint.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +1 -5 | 1.23 | src/colvarbias_meta.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +2 -4 | 1.4 | src/colvarbias_histogram.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +0 -3 | 1.7 | src/colvarbias_alb.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +6 -6 | 1.23 | src/colvarbias_abf.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +12 -15 | 1.16 | src/colvaratoms.h | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +23 -57 | 1.26 | src/colvaratoms.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +7 -20 | 1.34 | src/colvar.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +1 -1 | 1.51 | src/ScriptTcl.h | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/21 20:15:50 | jim | +20 -17 | 1.123 | src/ScriptTcl.C | Update Colvars to 9458d20a224744c9200f9d5ddb9b5b18765a2707 |
| 2017/03/20 19:52:17 | jim | +4 -2 | 1.1247 | src/SimParameters.h | From Joao Ribeiro, add IMDignoreForces option for QwikMD. |
| 2017/03/20 19:52:17 | jim | +11 -5 | 1.1477 | src/SimParameters.C | From Joao Ribeiro, add IMDignoreForces option for QwikMD. |
| 2017/03/20 19:52:17 | jim | +1 -1 | 1.15 | src/IMDOutput.C | From Joao Ribeiro, add IMDignoreForces option for QwikMD. |
| 2017/03/20 19:52:17 | jim | +4 -1 | 1.6 | src/GlobalMasterIMD.h | From Joao Ribeiro, add IMDignoreForces option for QwikMD. |
| 2017/03/20 19:52:17 | jim | +10 -4 | 1.10 | src/GlobalMasterIMD.C | From Joao Ribeiro, add IMDignoreForces option for QwikMD. |
| 2017/03/20 19:52:17 | jim | +2 -2 | 1.1132 | src/ComputeMgr.C | From Joao Ribeiro, add IMDignoreForces option for QwikMD. |
| 2017/03/08 23:29:30 | jim | +2 -1 | 1.36 | psfgen/src/tcl_psfgen.c | Fix C++-style variable declarations after first statement. |
| 2017/03/08 18:57:26 | jim | +1 -0 | 1.3 | ug/ug_colvars-cv.tex | Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 |
| 2017/03/08 18:57:23 | jim | +12 -1 | 1.9 | src/colvarscript.C | Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 |
| 2017/03/08 18:57:23 | jim | +4 -1 | 1.28 | src/colvarmodule.h | Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 |
| 2017/03/08 18:57:23 | jim | +11 -6 | 1.30 | src/colvarmodule.C | Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 |
| 2017/03/08 18:57:23 | jim | +14 -5 | 1.3 | src/colvardeps.h | Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 |
| 2017/03/08 18:57:23 | jim | +21 -24 | 1.5 | src/colvardeps.C | Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 |
| 2017/03/08 18:57:23 | jim | +21 -0 | 1.19 | src/colvarcomp_distances.C | Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 |
| 2017/03/08 18:57:23 | jim | +9 -0 | 1.25 | src/colvarcomp.h | Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 |
| 2017/03/08 18:57:23 | jim | +1 -1 | 1.25 | src/colvaratoms.C | Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 |
| 2017/03/08 18:57:23 | jim | +5 -5 | 1.33 | src/colvar.C | Update Colvars to f4e0a8eefb7790b7e7a17766cd0069d939c76041 |
| 2017/03/01 14:34:08 | jim | +17 -3 | 1.33 | ug/ug_colvars.tex | Update Colvars to 7c48dc02460f1f68a00c872acd964b5ff2276098 |
| 2017/03/01 14:34:00 | jim | +1 -1 | 1.27 | src/colvarmodule.h | Update Colvars to 7c48dc02460f1f68a00c872acd964b5ff2276098 |
| 2017/03/01 14:34:00 | jim | +6 -0 | 1.6 | src/colvarbias_restraint.h | Update Colvars to 7c48dc02460f1f68a00c872acd964b5ff2276098 |
| 2017/03/01 14:34:00 | jim | +33 -11 | 1.6 | src/colvarbias_restraint.C | Update Colvars to 7c48dc02460f1f68a00c872acd964b5ff2276098 |
| 2017/03/01 14:34:00 | jim | +19 -19 | 1.32 | src/colvar.C | Update Colvars to 7c48dc02460f1f68a00c872acd964b5ff2276098 |
| 2017/02/19 15:19:58 | jim | +75 -16 | 1.229 | src/ComputePme.C | Use CkLoop parallelization on slab PME trans, untrans, and ungrid sends. |
| 2017/02/17 17:19:05 | jim | +5 -5 | 1.228 | src/ComputePme.C | Change "Bool useCkLoop" to "int useCkLoop". |
| 2017/02/15 18:26:12 | jim | +19 -1 | 1.111 | config | Add --cuda-dlink option to specify gencode options to dlink cuFFT static library. |
| 2017/02/15 18:24:38 | jim | +5 -2 | 1.9 | arch/MacOSX-x86_64.cuda | Support CUDA 8.0, which requires different gencode options to dlink cuFFT static library. |
| 2017/02/15 18:24:38 | jim | +6 -3 | 1.16 | arch/Linux-x86_64.cuda | Support CUDA 8.0, which requires different gencode options to dlink cuFFT static library. |
| 2017/02/15 18:24:29 | jim | +1 -1 | 1.1359 | Makefile | Support CUDA 8.0, which requires different gencode options to dlink cuFFT static library. |
| 2017/02/08 22:56:16 | jim | +3 -4 | 1.15 | README.txt | Replace BioCoRE with ARBD and Lattice Microbes. |
| 2017/02/08 16:58:36 | jim | +7 -0 | 1.8 | ug/ug_colvars_macros.tex | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:36 | jim | +65 -51 | 1.32 | ug/ug_colvars.tex | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:35 | jim | +2 -2 | 1.5 | ug/ug_colvars.bib | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:35 | jim | +7 -0 | 1.2 | ug/ug_colvars-cv.tex | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +31 -24 | 1.15 | src/colvarvalue.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +10 -52 | 1.10 | src/colvarvalue.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +7 -0 | 1.16 | src/colvartypes.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +7 -0 | 1.6 | src/colvartypes.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +11 -0 | 1.5 | src/colvarscript.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +101 -12 | 1.8 | src/colvarscript.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +9 -2 | 1.16 | src/colvarproxy_namd.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +32 -12 | 1.27 | src/colvarproxy_namd.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +31 -6 | 1.17 | src/colvarproxy.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +8 -2 | 1.10 | src/colvarparse.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +11 -4 | 1.12 | src/colvarparse.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +87 -30 | 1.26 | src/colvarmodule.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +229 -94 | 1.29 | src/colvarmodule.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +35 -24 | 1.17 | src/colvargrid.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +10 -2 | 1.10 | src/colvargrid.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +16 -6 | 1.2 | src/colvardeps.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +46 -21 | 1.4 | src/colvardeps.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +7 -0 | 1.18 | src/colvarcomp_rotations.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +7 -0 | 1.14 | src/colvarcomp_protein.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +8 -0 | 1.18 | src/colvarcomp_distances.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:31 | jim | +7 -0 | 1.14 | src/colvarcomp_coordnums.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +7 -0 | 1.15 | src/colvarcomp_angles.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +7 -0 | 1.24 | src/colvarcomp.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +22 -0 | 1.12 | src/colvarcomp.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +192 -66 | 1.5 | src/colvarbias_restraint.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +907 -356 | 1.5 | src/colvarbias_restraint.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +35 -17 | 1.16 | src/colvarbias_meta.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +358 -320 | 1.22 | src/colvarbias_meta.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +9 -2 | 1.3 | src/colvarbias_histogram.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +16 -62 | 1.3 | src/colvarbias_histogram.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +11 -3 | 1.4 | src/colvarbias_alb.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +15 -49 | 1.6 | src/colvarbias_alb.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +9 -2 | 1.14 | src/colvarbias_abf.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +25 -91 | 1.22 | src/colvarbias_abf.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +93 -20 | 1.16 | src/colvarbias.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +161 -31 | 1.19 | src/colvarbias.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +7 -0 | 1.15 | src/colvaratoms.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +14 -5 | 1.24 | src/colvaratoms.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +44 -6 | 1.18 | src/colvar.h | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:30 | jim | +248 -175 | 1.31 | src/colvar.C | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/08 16:58:26 | jim | +1 -2 | 1.195 | Make.depends | Update Colvars to 455664c50ff777fbd0cf7c8947f87063c9085d05 |
| 2017/02/06 18:54:16 | jim | +5 -2 | 1.28 | ug/ug.bib | Fix "page" to "pages". |
| 2017/02/06 18:51:34 | jim | +7 -3 | 1.27 | ug/ug.bib | Add volume and page to GaMD reference. |
| 2017/02/03 21:39:32 | jim | None | 1.1 | ug/figures/GaMD-scheme.jpg | Gaussian accelerated MD (GaMD) implementation by Andrew Pang and Yi Wang. |
| 2017/02/03 21:39:29 | jim | +150 -0 | 1.18 | ug/ug_accel.tex | Gaussian accelerated MD (GaMD) implementation by Andrew Pang and Yi Wang. |
| 2017/02/03 21:39:29 | jim | +21 -2 | 1.26 | ug/ug.bib | Gaussian accelerated MD (GaMD) implementation by Andrew Pang and Yi Wang. |
| 2017/02/03 21:39:23 | jim | +14 -2 | 1.1246 | src/SimParameters.h | Gaussian accelerated MD (GaMD) implementation by Andrew Pang and Yi Wang. |
| 2017/02/03 21:39:23 | jim | +109 -9 | 1.1476 | src/SimParameters.C | Gaussian accelerated MD (GaMD) implementation by Andrew Pang and Yi Wang. |
| 2017/02/03 21:39:23 | jim | +16 -0 | 1.1092 | src/Controller.h | Gaussian accelerated MD (GaMD) implementation by Andrew Pang and Yi Wang. |
| 2017/02/03 21:39:23 | jim | +453 -46 | 1.1325 | src/Controller.C | Gaussian accelerated MD (GaMD) implementation by Andrew Pang and Yi Wang. |
| 2017/01/25 21:41:12 | jim | +32 -0 | 1.10 | psfgen/src/topo_defs.c | Warn and ignore on self and duplicate bonds when reading topology files. |
| 2017/01/13 18:56:37 | jim | +2 -2 | 1.35 | psfgen/src/tcl_psfgen.c | Bump version to 1.6.6. |
| 2017/01/13 00:30:07 | jim | +10 -0 | 1.34 | psfgen/src/tcl_psfgen.c | From Brian Radak, extend segment command to query charge. |
| 2017/01/13 00:30:05 | jim | +1 -0 | 1.16 | psfgen/doc/ug_psfgen.tex | From Brian Radak, extend segment command to query charge. |
| 2017/01/13 00:24:44 | jim | +3 -1 | 1.25 | psfgen/src/topo_mol.c | In topology file PRES (patch) entries support ATOM record with name but no type or charge to specify subsequent atom insertion order. |
| 2017/01/13 00:24:44 | jim | +6 -1 | 1.11 | psfgen/src/charmm_parse_topo_defs.c | In topology file PRES (patch) entries support ATOM record with name but no type or charge to specify subsequent atom insertion order. |
| 2017/01/10 22:35:34 | jim | +1 -1 | 1.5 | src/MoleculeQM.C | Add space in nested template to appease xlC compiler. |
| 2017/01/09 17:19:34 | jim | +17 -14 | 1.10 | psfgen/src/charmm_parse_topo_defs.c | Recognize READ statements even if previous END statement is missing. |
| 2016/12/21 16:57:00 | jim | +34 -2 | 1.33 | ug/ug_runit.tex | Update for Omni-Path and KNL. |
| 2016/12/21 16:56:56 | jim | +28 -0 | 1.120 | notes.txt | Update for Omni-Path and KNL. |
| 2016/12/21 15:42:26 | jim | +1 -1 | 1.74 | ug/Makefile | Update to 2.12. |
| 2016/12/21 15:42:24 | jim | +5 -5 | 1.119 | notes.txt | Update to 2.12. |
| 2016/12/21 15:42:24 | jim | +3 -3 | 1.66 | announce.txt | Update to 2.12. |
| 2016/12/21 15:42:24 | jim | +1 -1 | 1.1358 | Makefile | Update to 2.12. |
| 2016/12/21 13:51:06 | jim | +1 -1 | 1.25 | src/colvarmodule.h | Fixes from Jerome Henin to the total force calculation in ABF and wall potentials for extended-Lagrangian coordinates. |
| 2016/12/21 13:51:06 | jim | +38 -26 | 1.30 | src/colvar.C | Fixes from Jerome Henin to the total force calculation in ABF and wall potentials for extended-Lagrangian coordinates. |
| 2016/12/20 21:43:13 | jim | +11 -0 | 1.24 | psfgen/src/topo_mol.c | Fix "psfset segid" to update hash table. |
| 2016/12/20 20:36:33 | jim | +1 -1 | 1.17 | ug/namd_macros.tex | Add authors Bernardi, Fu, Melo, Rudack. |
| 2016/12/20 20:33:10 | jim | +1 -1 | 1.73 | ug/Makefile | Remove unused ug_eabf.tex file to avoid confusion. |
| 2016/12/20 20:25:53 | jim | +4 -3 | 1.31 | ug/ug_colvars.tex | Update eABF docs for recent changes. |
| 2016/12/20 06:11:14 | jim | +2 -2 | 1.33 | psfgen/src/tcl_psfgen.c | Bump version to 1.6.5. |
| 2016/12/20 06:01:23 | jim | +14 -2 | 1.10 | psfgen/src/topo_mol.h | From Brian Radak, replace new "vel" and "bfactor" commands with "psfset". |
| 2016/12/20 06:01:23 | jim | +58 -2 | 1.23 | psfgen/src/topo_mol.c | From Brian Radak, replace new "vel" and "bfactor" commands with "psfset". |
| 2016/12/20 06:01:23 | jim | +83 -98 | 1.32 | psfgen/src/tcl_psfgen.c | From Brian Radak, replace new "vel" and "bfactor" commands with "psfset". |
| 2016/12/20 06:01:18 | jim | +20 -23 | 1.15 | psfgen/doc/ug_psfgen.tex | From Brian Radak, replace new "vel" and "bfactor" commands with "psfset". |
| 2016/12/18 21:34:50 | jim | +88 -25 | 1.2 | lib/eabf/eabf.tcl | eABF changes from Chris Chipot: count files properly outputted; -mergesplitwindow takes eabf files rather than grad files; change range of windows via colvarsInput keyword, leave eabf_inputname zero, use -mergesplitwindow to combine. |
| 2016/12/18 21:19:05 | jim | +14 -3 | 1.2 | src/eabf2D.C | From Chris Chipot, eABF count files are now properly outputted. |
| 2016/12/18 21:19:04 | jim | +9 -0 | 1.2 | src/eabf1D.C | From Chris Chipot, eABF count files are now properly outputted. |
| 2016/12/16 22:35:26 | jim | +9 -0 | 1.3 | arch/Linux-KNL-icc.arch | Avoid Intel 17.0 compiler due to apparent vectorization bug. |
| 2016/12/16 22:00:47 | jim | +6 -0 | 1.2 | arch/CRAY-XC-KNL-intel.arch | Avoid Intel 17.0 compiler due to apparent vectorization bug. |
| 2016/12/15 21:09:24 | jim | +41 -16 | 1.14 | psfgen/doc/ug_psfgen.tex | Document vel, bfactor, and renameatom commands and writepsf nopatches option. |
| 2016/12/06 21:31:46 | jim | +1 -1 | 1.14 | src/ComputeLCPO.C | Fix apparent error in SASA gradient calculation noticed by Kecheng Yang. |
| 2016/12/05 22:20:43 | jim | +2 -2 | 1.2 | src/CudaTileListKernel.cu | Remove unnecessary safety check. |
| 2016/11/28 17:32:06 | jim | +3 -5 | 1.7 | ug/ug_colvars_macros.tex | Colvars doc fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:32:06 | jim | +8 -8 | 1.30 | ug/ug_colvars.tex | Colvars doc fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +3 -0 | 1.14 | src/colvarvalue.h | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +33 -0 | 1.9 | src/colvarvalue.C | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +1 -1 | 1.15 | src/colvarproxy_namd.h | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +1 -1 | 1.26 | src/colvarproxy_namd.C | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +1 -1 | 1.16 | src/colvarproxy.h | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +3 -3 | 1.24 | src/colvarmodule.h | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +1 -1 | 1.28 | src/colvarmodule.C | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +41 -3 | 1.16 | src/colvargrid.h | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +14 -0 | 1.9 | src/colvargrid.C | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +5 -0 | 1.3 | src/colvardeps.C | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +73 -0 | 1.17 | src/colvarcomp_rotations.C | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +23 -6 | 1.13 | src/colvarcomp_protein.C | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +117 -1 | 1.17 | src/colvarcomp_distances.C | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +21 -10 | 1.13 | src/colvarcomp_coordnums.C | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +50 -0 | 1.14 | src/colvarcomp_angles.C | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +70 -314 | 1.23 | src/colvarcomp.h | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +33 -4 | 1.11 | src/colvarcomp.C | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +25 -2 | 1.21 | src/colvarbias_meta.C | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +3 -1 | 1.14 | src/colvaratoms.h | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +6 -1 | 1.23 | src/colvaratoms.C | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/28 17:30:57 | jim | +7 -4 | 1.29 | src/colvar.C | Colvars fixes from Giacomo Fiorin and Jerome Henin. |
| 2016/11/24 00:49:54 | jim | +4 -0 | 1.1091 | src/NamdState.C | From Marcelo Melo: Fixed bug in execution of user-defined QM software. Error on incompatibility with CUDA build. Minor improvements in output. |
| 2016/11/24 00:49:53 | jim | +5 -4 | 1.4 | src/MoleculeQM.C | From Marcelo Melo: Fixed bug in execution of user-defined QM software. Error on incompatibility with CUDA build. Minor improvements in output. |
| 2016/11/24 00:49:52 | jim | +50 -29 | 1.4 | src/ComputeQM.C | From Marcelo Melo: Fixed bug in execution of user-defined QM software. Error on incompatibility with CUDA build. Minor improvements in output. |
| 2016/11/14 20:24:41 | jim | +3 -2 | 1.1245 | src/SimParameters.h | From Marcelo Melo, changes to the execution of selected quantum chemistry software to work around a bug in ORCA, changes in default keyword values for clarity (from user feedback). |
| 2016/11/14 20:24:41 | jim | +12 -6 | 1.1475 | src/SimParameters.C | From Marcelo Melo, changes to the execution of selected quantum chemistry software to work around a bug in ORCA, changes in default keyword values for clarity (from user feedback). |
| 2016/11/14 20:24:41 | jim | +1 -1 | 1.3 | src/MoleculeQM.C | From Marcelo Melo, changes to the execution of selected quantum chemistry software to work around a bug in ORCA, changes in default keyword values for clarity (from user feedback). |
| 2016/11/14 20:24:41 | jim | +5 -1 | 1.1265 | src/Molecule.C | From Marcelo Melo, changes to the execution of selected quantum chemistry software to work around a bug in ORCA, changes in default keyword values for clarity (from user feedback). |
| 2016/11/14 20:24:40 | jim | +26 -13 | 1.3 | src/ComputeQM.C | From Marcelo Melo, changes to the execution of selected quantum chemistry software to work around a bug in ORCA, changes in default keyword values for clarity (from user feedback). |
| 2016/11/10 22:18:30 | jim | +1 -1 | 1.15 | arch/Linux-x86_64.cuda | Add gencode flags for compute_30 support. |
| 2016/11/07 20:28:33 | jim | +59 -59 | 1.34 | ug/ug_alchemy.tex | From Brian Radak, change alchBondLambdaEnd default and update thermodynamic integration documentation. |
| 2016/11/07 20:26:15 | jim | +3 -3 | 1.1474 | src/SimParameters.C | From Brian Radak per discussion with Chris Chipot, change the default for alchBondLambdaEnd to be 0 (i.e. no scaling). |
| 2016/11/06 21:50:29 | jim | +1 -1 | 1.22 | psfgen/src/topo_mol.c | Fix uninitialized pointer bug. |
| 2016/11/05 15:42:09 | jim | +2 -0 | 1.23 | src/PmeKSpace.C | Limit CkLoop minimum grainsize. |
| 2016/11/05 15:14:11 | jim | +4 -3 | 1.22 | src/PmeKSpace.C | Fix bad CkLoop code that was assuming one part per chunk. |
| 2016/11/04 21:08:08 | jim | +2 -3 | 1.118 | notes.txt | Remove reference to BioCoRE. |
| 2016/11/04 01:25:07 | jim | +1 -1 | 1.227 | src/ComputePme.C | Fix bug that was enabling PME k-space CkLoop code on too few pes. |
| 2016/11/01 22:01:13 | jim | +1 -1 | 1.72 | ug/Makefile | Update to 2.12b1. |
| 2016/11/01 22:01:10 | jim | +5 -5 | 1.117 | notes.txt | Update to 2.12b1. |
| 2016/11/01 22:01:10 | jim | +25 -39 | 1.65 | announce.txt | Update to 2.12b1. |
| 2016/11/01 22:01:10 | jim | +1 -1 | 1.1357 | Makefile | Update to 2.12b1. |
| 2016/10/30 22:50:03 | jim | +1 -1 | 1.8 | src/fftlib.C | Auto-enable useCkLoop for thread-parallel PME when it makes sense. |
| 2016/10/30 22:50:02 | jim | +8 -3 | 1.1473 | src/SimParameters.C | Auto-enable useCkLoop for thread-parallel PME when it makes sense. |
| 2016/10/30 22:50:02 | jim | +1 -1 | 1.14 | src/PmeKSpace.h | Auto-enable useCkLoop for thread-parallel PME when it makes sense. |
| 2016/10/30 22:50:02 | jim | +2 -3 | 1.21 | src/PmeKSpace.C | Auto-enable useCkLoop for thread-parallel PME when it makes sense. |
| 2016/10/30 22:50:02 | jim | +2 -0 | 1.1154 | src/Node.C | Auto-enable useCkLoop for thread-parallel PME when it makes sense. |
| 2016/10/30 22:50:00 | jim | +40 -13 | 1.226 | src/ComputePme.C | Auto-enable useCkLoop for thread-parallel PME when it makes sense. |
| 2016/10/27 22:05:36 | jim | +17 -2 | 1.1472 | src/SimParameters.C | Disable new CUDA kernels for non-orthorhombic cells. |
| 2016/10/27 22:04:05 | jim | +4 -4 | 1.2 | src/CudaPmeSolverUtil.C | Fix spelling of "orthorhombic". |
| 2016/10/27 21:12:14 | jim | +4 -4 | 1.5 | src/DeviceCUDA.C | Require CUDA compute capability 3.0 or higher. |
| 2016/10/27 21:12:14 | jim | +4 -4 | 1.102 | src/ComputeNonbondedCUDA.C | Require CUDA compute capability 3.0 or higher. |
| 2016/10/27 20:26:29 | jim | +8 -4 | 1.1471 | src/SimParameters.C | By default enable new CUDA nonbonded kernel always (disable with useCUDA2 off)and for 1-4 physical nodes also new CUDA PME kernel (disable with usePMECUDA off). |
| 2016/10/27 18:17:29 | jim | +5 -2 | 1.225 | src/ComputePme.C | Make old CUDA PME (PMEOffload) compatible with new CUDA nonbonded kernels (useCUDA2). |
| 2016/10/27 18:16:41 | jim | +3 -1 | 1.2 | src/CudaComputeNonbonded.C | Comment out code to avoid PME pes because it delays results for those pes. |
| 2016/10/24 21:16:00 | jim | +10 -1 | 1.29 | ug/ug_colvars.tex | From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). |
| 2016/10/24 21:15:58 | jim | +30 -0 | 1.7 | src/colvarscript.C | From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). |
| 2016/10/24 21:15:58 | jim | +5 -2 | 1.14 | src/colvarproxy_namd.h | From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). |
| 2016/10/24 21:15:58 | jim | +3 -3 | 1.25 | src/colvarproxy_namd.C | From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). |
| 2016/10/24 21:15:58 | jim | +5 -2 | 1.15 | src/colvarproxy.h | From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). |
| 2016/10/24 21:15:58 | jim | +6 -6 | 1.11 | src/colvarparse.C | From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). |
| 2016/10/24 21:15:58 | jim | +1 -1 | 1.23 | src/colvarmodule.h | From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). |
| 2016/10/24 21:15:58 | jim | +6 -0 | 1.27 | src/colvarmodule.C | From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). |
| 2016/10/24 21:15:58 | jim | +4 -2 | 1.2 | src/colvardeps.C | From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). |
| 2016/10/24 21:15:58 | jim | +3 -6 | 1.10 | src/colvarcomp.C | From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). |
| 2016/10/24 21:15:57 | jim | +8 -0 | 1.15 | src/colvarbias_meta.h | From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). |
| 2016/10/24 21:15:57 | jim | +52 -32 | 1.20 | src/colvarbias_meta.C | From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). |
| 2016/10/24 21:15:57 | jim | +2 -1 | 1.21 | src/colvarbias_abf.C | From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). |
| 2016/10/24 21:15:57 | jim | +17 -7 | 1.22 | src/colvaratoms.C | From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). |
| 2016/10/24 21:15:57 | jim | +9 -3 | 1.28 | src/colvar.C | From Giacomo Fiorin, fixed calculation of atomic forces for distanceDir and distanceVec colvars in scalable COM case; introduced "SMP on|off" option to control whether CkLoop is used by Colvars at runtime; subtractAppliedForce now handles extended-Lagrangian system force calculation (Jerome Henin); implemented ensemble-biased metadynamics (Fabrizio Marinelli, NIH). |
| 2016/10/21 21:49:57 | jim | +7 -0 | 1.1093 | src/ComputeNonbondedUtil.h | Implement MARTINI switching function for Lennard-Jones in KNL kernel. |
| 2016/10/21 21:49:56 | jim | +25 -0 | 1.1125 | src/ComputeNonbondedUtil.C | Implement MARTINI switching function for Lennard-Jones in KNL kernel. |
| 2016/10/21 21:49:56 | jim | +33 -12 | 1.6 | src/ComputeNonbondedBase2KNL.h | Implement MARTINI switching function for Lennard-Jones in KNL kernel. |
| 2016/10/20 21:20:09 | jim | +35 -0 | 1.8 | license.txt | Append CUB license. |
| 2016/10/20 20:50:56 | jim | +1 -0 | 1.110 | config | Recognize ofi in Charm++ platform and add to NAMD platform string. |
| 2016/10/20 20:15:36 | jim | +0 -3 | 1.2 | lib/eabf/example/co.in | Fix from Chris Chipot for eABF example due to recent Colvars changes. |
| 2016/10/14 16:35:16 | jim | +1 -1 | 1.13 | src/colvarproxy_namd.h | From Giacomo Fiorin and Jerome Henin, fix incorrect inizialization of atoms from PDB file and wrong wall forces for eABF. |
| 2016/10/14 16:35:16 | jim | +1 -1 | 1.24 | src/colvarproxy_namd.C | From Giacomo Fiorin and Jerome Henin, fix incorrect inizialization of atoms from PDB file and wrong wall forces for eABF. |
| 2016/10/14 16:35:16 | jim | +4 -1 | 1.22 | src/colvarmodule.h | From Giacomo Fiorin and Jerome Henin, fix incorrect inizialization of atoms from PDB file and wrong wall forces for eABF. |
| 2016/10/14 16:35:16 | jim | +2 -0 | 1.13 | src/colvaratoms.h | From Giacomo Fiorin and Jerome Henin, fix incorrect inizialization of atoms from PDB file and wrong wall forces for eABF. |
| 2016/10/14 16:35:15 | jim | +23 -0 | 1.21 | src/colvaratoms.C | From Giacomo Fiorin and Jerome Henin, fix incorrect inizialization of atoms from PDB file and wrong wall forces for eABF. |
| 2016/10/14 16:35:15 | jim | +4 -4 | 1.27 | src/colvar.C | From Giacomo Fiorin and Jerome Henin, fix incorrect inizialization of atoms from PDB file and wrong wall forces for eABF. |
| 2016/10/14 16:12:12 | jim | +5 -5 | 1.1324 | src/Controller.C | From Brian Radak, alchemical output format tweaks and make TI output behave more like FEP output. |
| 2016/10/10 19:52:01 | jim | +2 -2 | 1.224 | src/ComputePme.C | Work around CUDA errors during PME force calculation by using stream 0 for potential upload. |
| 2016/10/07 21:46:27 | jim | +1 -1 | 1.28 | ug/ug_colvars.tex | Fix missing reference. |
| 2016/10/07 21:45:01 | jim | +3 -3 | 1.6 | ug/ug_colvars_macros.tex | Tweak index entries and fix missing references. |
| 2016/10/07 21:42:39 | jim | +1 -1 | 1.71 | ug/Makefile | Add dependency. |
| 2016/10/07 16:14:21 | jim | +418 -428 | 1.2 | ug/figures/colvars_diagram.pdf | 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 |
| 2016/10/07 16:14:21 | jim | None | 1.1 | ug/figures/amd_schematic.jpg | 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 |
| 2016/10/07 16:14:18 | jim | +10 -41 | 1.5 | ug/ug_colvars_macros.tex | 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 |
| 2016/10/07 16:14:18 | jim | +1060 -309 | 1.27 | ug/ug_colvars.tex | 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 |
| 2016/10/07 16:14:18 | jim | +69 -0 | 1.4 | ug/ug_colvars.bib | 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 |
| 2016/10/07 16:14:18 | jim | None | 1.1 | ug/ug_colvars-cv.tex | 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 |
| 2016/10/07 16:14:08 | jim | +1 -1 | 1.13 | src/colvarvalue.h | 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 |
| 2016/10/07 16:14:08 | jim | +1 -1 | 1.8 | src/colvarvalue.C | 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 |
| 2016/10/07 16:14:08 | jim | +40 -6 | 1.15 | src/colvartypes.h | 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 |
| 2016/10/07 16:14:08 | jim | +50 -57 | 1.5 | src/colvartypes.C | 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 |
| 2016/10/07 16:14:08 | jim | +2 -1 | 1.4 | src/colvarscript.h | 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 |
| 2016/10/07 16:14:08 | jim | +76 -43 | 1.6 | src/colvarscript.C | 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 |
| 2016/10/07 16:14:08 | jim | +125 -35 | 1.12 | src/colvarproxy_namd.h | 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 |
| 2016/10/07 16:14:08 | jim | +541 -250 | 1.23 | src/colvarproxy_namd.C | 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 |
| 2016/10/07 16:14:08 | jim | +449 -113 | 1.14 | src/colvarproxy.h | 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 |
| 2016/10/07 16:14:08 | jim | +149 -55 | 1.9 | src/colvarparse.h | 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 |
| 2016/10/07 16:14:08 | jim | +397 -253 | 1.10 | src/colvarparse.C | 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 |
| 2016/10/07 16:14:08 | jim | +94 -46 | 1.21 | src/colvarmodule.h | 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 |
| 2016/10/07 16:14:08 | jim | +471 -152 | 1.26 | src/colvarmodule.C | 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 |
| 2016/10/07 16:14:08 | jim | +140 -84 | 1.15 | src/colvargrid.h | 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 |
| 2016/10/07 16:14:08 | jim | +4 -5 | 1.8 | src/colvargrid.C | 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 |
| 2016/10/07 16:14:08 | jim | None | 1.1 | src/colvardeps.h | 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 |
| 2016/10/07 16:14:08 | jim | None | 1.1 | src/colvardeps.C | 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 |
| 2016/10/07 16:14:08 | jim | +45 -70 | 1.16 | src/colvarcomp_rotations.C | 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 |
| 2016/10/07 16:14:08 | jim | +13 -3 | 1.12 | src/colvarcomp_protein.C | 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 |
| 2016/10/07 16:14:08 | jim | +317 -351 | 1.16 | src/colvarcomp_distances.C | 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 |
| 2016/10/07 16:14:08 | jim | +194 -52 | 1.12 | src/colvarcomp_coordnums.C | 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 |
| 2016/10/07 16:14:08 | jim | +197 -112 | 1.13 | src/colvarcomp_angles.C | 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 |
| 2016/10/07 16:14:08 | jim | +158 -63 | 1.22 | src/colvarcomp.h | 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 |
| 2016/10/07 16:14:08 | jim | +188 -92 | 1.9 | src/colvarcomp.C | 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 |
| 2016/10/07 16:14:08 | jim | +80 -14 | 1.4 | src/colvarbias_restraint.h | 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 |
| 2016/10/07 16:14:08 | jim | +333 -24 | 1.4 | src/colvarbias_restraint.C | 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 |
| 2016/10/07 16:14:08 | jim | +5 -15 | 1.14 | src/colvarbias_meta.h | 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 |
| 2016/10/07 16:14:07 | jim | +33 -20 | 1.19 | src/colvarbias_meta.C | 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 |
| 2016/10/07 16:14:07 | jim | +6 -7 | 1.2 | src/colvarbias_histogram.h | 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 |
| 2016/10/07 16:14:07 | jim | +40 -20 | 1.2 | src/colvarbias_histogram.C | 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 |
| 2016/10/07 16:14:07 | jim | +4 -11 | 1.3 | src/colvarbias_alb.h | 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 |
| 2016/10/07 16:14:07 | jim | +33 -16 | 1.5 | src/colvarbias_alb.C | 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 |
| 2016/10/07 16:14:07 | jim | +32 -8 | 1.13 | src/colvarbias_abf.h | 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 |
| 2016/10/07 16:14:07 | jim | +239 -57 | 1.20 | src/colvarbias_abf.C | 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 |
| 2016/10/07 16:14:07 | jim | +40 -7 | 1.15 | src/colvarbias.h | 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 |
| 2016/10/07 16:14:07 | jim | +111 -36 | 1.18 | src/colvarbias.C | 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 |
| 2016/10/07 16:14:07 | jim | +248 -120 | 1.12 | src/colvaratoms.h | 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 |
| 2016/10/07 16:14:07 | jim | +711 -412 | 1.20 | src/colvaratoms.C | 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 |
| 2016/10/07 16:14:07 | jim | +108 -105 | 1.17 | src/colvar.h | 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 |
| 2016/10/07 16:14:05 | jim | +689 -670 | 1.26 | src/colvar.C | 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 |
| 2016/10/07 16:14:01 | jim | +1 -0 | 1.1356 | Makefile | 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 |
| 2016/10/07 16:14:00 | jim | +34 -4 | 1.194 | Make.depends | 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 |
| 2016/10/07 15:54:01 | jim | +2 -2 | 1.22 | ug/ug.tex | Remove separate eABF docs now included with colvars. |
| 2016/09/30 20:04:33 | jim | +4 -0 | 1.33 | ug/ug_start.tex | Document move command. |
| 2016/09/30 18:35:12 | jim | +27 -0 | 1.1264 | src/Molecule.C | Initialize QM/MM pointers to zero to avoid crash when reloading structure. |
| 2016/09/29 22:43:40 | jim | +1 -1 | 1.5 | psfgen/src/topo_mol_output.h | Add "nopatches" option to writepsf to reduce number of REMARKS lines. |
| 2016/09/29 22:43:40 | jim | +3 -1 | 1.15 | psfgen/src/topo_mol_output.c | Add "nopatches" option to writepsf to reduce number of REMARKS lines. |
| 2016/09/29 22:43:40 | jim | +5 -3 | 1.31 | psfgen/src/tcl_psfgen.c | Add "nopatches" option to writepsf to reduce number of REMARKS lines. |
| 2016/09/29 22:29:50 | jim | +7 -0 | 1.1091 | src/Controller.h | From Brian Radak: cumulative alchemical work is now printed out in the TI log when alchemical switching is on; energy evaluations at alchLambda2 are now printed in their own FEP log during FEP. |
| 2016/09/29 22:29:50 | jim | +53 -29 | 1.1323 | src/Controller.C | From Brian Radak: cumulative alchemical work is now printed out in the TI log when alchemical switching is on; energy evaluations at alchLambda2 are now printed in their own FEP log during FEP. |
| 2016/09/29 21:58:45 | jim | +2 -2 | 1.3 | arch/Linux-ARM-g++.arch | Add -std=c++11 to compiler options. |
| 2016/09/29 21:58:44 | jim | +1 -1 | 1.2 | arch/Linux-ARM64-g++.arch | Add -std=c++11 to compiler options. |
| 2016/09/29 21:30:48 | jim | +25 -25 | 1.1470 | src/SimParameters.C | Replace "not" and "and" with "!" and "&&" for MSVC since macros annoy g++. |
| 2016/09/29 21:30:47 | jim | +25 -25 | 1.2 | src/MoleculeQM.C | Replace "not" and "and" with "!" and "&&" for MSVC since macros annoy g++. |
| 2016/09/29 21:30:47 | jim | +1 -1 | 1.1238 | src/HomePatch.C | Replace "not" and "and" with "!" and "&&" for MSVC since macros annoy g++. |
| 2016/09/29 21:10:34 | jim | +20 -23 | 1.2 | src/ComputeQM.C | Replace "not" and "and" with "!" and "&&" for MSVC since macros annoy g++. |
| 2016/09/29 20:31:47 | jim | +1 -0 | 1.1031 | src/main.ci | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +5 -2 | 1.1290 | src/WorkDistrib.C | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +48 -2 | 1.1244 | src/SimParameters.h | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +395 -5 | 1.1469 | src/SimParameters.C | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +21 -0 | 1.1090 | src/NamdState.C | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | None | 1.1 | src/MoleculeQM.C | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +194 -0 | 1.1120 | src/Molecule.h | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +227 -15 | 1.1263 | src/Molecule.C | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +4 -0 | 1.1090 | src/HomePatch.h | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +64 -0 | 1.1237 | src/HomePatch.C | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +6 -4 | 1.1322 | src/Controller.C | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | None | 1.1 | src/ComputeQMMgr.ci | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | None | 1.1 | src/ComputeQM.h | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | None | 1.1 | src/ComputeQM.C | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +11 -0 | 1.37 | src/ComputePme.h | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +81 -0 | 1.223 | src/ComputePme.C | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +1 -0 | 1.1092 | src/ComputeNonbondedUtil.h | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +3 -0 | 1.1124 | src/ComputeNonbondedUtil.C | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +1 -0 | 1.1064 | src/ComputeNonbondedSelf.C | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +1 -0 | 1.55 | src/ComputeNonbondedBase2.h | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +48 -0 | 1.1192 | src/ComputeNonbondedBase.h | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +11 -2 | 1.1131 | src/ComputeMgr.C | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +1 -0 | 1.1059 | src/ComputeMap.h | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:47 | jim | +1 -0 | 1.79 | src/BackEnd.C | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:46 | jim | +1 -0 | 1.1034 | src/BOCgroup.h | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:43 | jim | +4 -0 | 1.1355 | Makefile | QM/MM interface from Marcelo Melo. |
| 2016/09/29 20:31:43 | jim | +144 -0 | 1.193 | Make.depends | QM/MM interface from Marcelo Melo. |
| 2016/09/27 22:26:15 | jim | +12 -2 | 1.1153 | src/Node.C | Preliminary fix for reloading structure with extraBonds. |
| 2016/09/27 20:51:27 | jim | +15 -29 | 1.2 | src/ComputePmeCUDAMgr.h | Fix from Antti-Pekka Hynninen for usePMECUDA hangs on Windows, other cleanup. |
| 2016/09/27 15:40:44 | jim | None | 1.1 | ug/ug_eabf.bib | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:44 | jim | +4 -1 | 1.21 | ug/ug.tex | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:44 | jim | +1 -1 | 1.70 | ug/Makefile | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:42 | jim | None | 1.1 | src/eabffunc.h | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:42 | jim | None | 1.1 | src/eabffunc.C | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:42 | jim | None | 1.1 | src/eabfTcl.C | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:42 | jim | None | 1.1 | src/eabf2D.h | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:42 | jim | None | 1.1 | src/eabf2D.C | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:42 | jim | None | 1.1 | src/eabf1D.h | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:41 | jim | None | 1.1 | src/eabf1D.C | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:41 | jim | None | 1.1 | src/eabf.h | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:41 | jim | +4 -0 | 1.122 | src/ScriptTcl.C | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:39 | jim | None | 1.1 | lib/eabf/example/co.in | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:39 | jim | None | 1.1 | lib/eabf/example/abf.namd | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:39 | jim | None | 1.1 | lib/eabf/example/CH_final.psf | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:39 | jim | None | 1.1 | lib/eabf/example/CH_final.pdb | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:39 | jim | None | 1.1 | lib/eabf/example/CH_cgenff.prm | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:35 | jim | None | 1.1 | lib/eabf/eabf.tcl | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:31 | jim | +4 -0 | 1.1354 | Makefile | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:40:31 | jim | +27 -0 | 1.192 | Make.depends | Extended Adaptive Biasing Force method from Haohao Fu and Christophe Chipot. |
| 2016/09/27 15:33:10 | jim | +6 -0 | 1.4 | src/fstream_namd.h | Add option to create backup file by passing extension to constructor or open(). |
| 2016/09/27 15:33:10 | jim | +6 -0 | 1.4 | src/fstream_namd.C | Add option to create backup file by passing extension to constructor or open(). |
| 2016/09/22 22:14:01 | jim | +5 -5 | 1.1091 | src/ComputeNonbondedUtil.h | Change temporary pairlists from short to int and use simple pairlist loops on KNL. |
| 2016/09/22 22:14:01 | jim | +13 -9 | 1.1191 | src/ComputeNonbondedBase.h | Change temporary pairlists from short to int and use simple pairlist loops on KNL. |
| 2016/09/21 20:40:53 | ryanmcgreevy | +34 -4 | 1.1468 | src/SimParameters.C | Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. |
| 2016/09/21 20:40:53 | ryanmcgreevy | +1 -0 | 1.50 | src/ScriptTcl.h | Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. |
| 2016/09/21 20:40:53 | ryanmcgreevy | +33 -0 | 1.121 | src/ScriptTcl.C | Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. |
| 2016/09/21 20:40:52 | ryanmcgreevy | +4 -0 | 1.1054 | src/Node.h | Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. |
| 2016/09/21 20:40:51 | ryanmcgreevy | +1 -0 | 1.1035 | src/Node.ci | Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. |
| 2016/09/21 20:40:51 | ryanmcgreevy | +42 -0 | 1.1152 | src/Node.C | Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. |
| 2016/09/21 20:40:51 | ryanmcgreevy | +3 -0 | 1.5 | src/MGridforceParams.h | Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. |
| 2016/09/21 20:40:51 | ryanmcgreevy | +29 -5 | 1.5 | src/MGridforceParams.C | Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. |
| 2016/09/21 20:40:51 | ryanmcgreevy | +13 -2 | 1.17 | src/GridForceGrid.h | Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. |
| 2016/09/21 20:40:48 | ryanmcgreevy | +8 -2 | 1.24 | src/GridForceGrid.C | Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. |
| 2016/09/21 20:40:42 | ryanmcgreevy | +1 -1 | 1.28 | src/ComputeGridForce.C | Update gscale parameter during runtime functionality added (from Chris Maffeo). gridforcechecksize now works for multiple grids. |
| 2016/09/20 20:33:19 | jim | +3 -3 | 1.30 | psfgen/src/tcl_psfgen.c | From Brian Radak, fix docs for psfgen segment queries. |
| 2016/09/20 20:33:12 | jim | +5 -3 | 1.13 | psfgen/doc/ug_psfgen.tex | From Brian Radak, fix docs for psfgen segment queries. |
| 2016/09/19 22:51:20 | jim | +6 -3 | 1.25 | ug/ug.bib | Fix error. |
| 2016/09/19 22:49:40 | jim | +1 -1 | 1.32 | ug/ug_start.tex | Fix multiply defined label. |
| 2016/09/19 21:45:24 | jim | +13 -1 | 1.29 | psfgen/src/tcl_psfgen.c | From Brian Radak, add ability to query atomid. |
| 2016/09/19 21:39:24 | jim | +1 -1 | 1.9 | src/sortreplicas.c | Fix bug where trajectory frames were sorted based on index of previous frame (caught by Wen Ma). |
| 2016/09/19 21:11:38 | jim | +4 -4 | 1.120 | src/ScriptTcl.C | Provide better error messages for config parameter processing called via Tcl unknown proc. |
| 2016/09/19 20:31:54 | jim | +6 -0 | 1.119 | src/ScriptTcl.C | Pass long and double from Python to Tcl as objects instead of strings. |
| 2016/09/19 17:58:32 | jim | +14 -3 | 1.109 | config | Add --python-prefix option, ignore Python 3 if installed. |
| 2016/09/19 17:39:17 | jim | +3 -2 | 1.1467 | src/SimParameters.C | From Brian Radak, make outputEnergies script-settable. |
| 2016/09/18 22:28:32 | jim | +2 -0 | 1.25 | src/mainfunc.C | Fix non-Tcl builds. |
| 2016/09/18 22:24:39 | jim | +12 -0 | 1.31 | ug/ug_start.tex | Add --tclmain and +tclsh options to allow passing of command-line arguments to a Tcl script either with (--tclmain) or without (+tclsh) Charm++ startup and NAMD scripting features. E.g., "./namd2 +tclsh script.tcl arg1 arg2". |
| 2016/09/18 22:24:34 | jim | +13 -0 | 1.24 | src/mainfunc.C | Add --tclmain and +tclsh options to allow passing of command-line arguments to a Tcl script either with (--tclmain) or without (+tclsh) Charm++ startup and NAMD scripting features. E.g., "./namd2 +tclsh script.tcl arg1 arg2". |
| 2016/09/18 22:24:33 | jim | +2 -0 | 1.49 | src/ScriptTcl.h | Add --tclmain and +tclsh options to allow passing of command-line arguments to a Tcl script either with (--tclmain) or without (+tclsh) Charm++ startup and NAMD scripting features. E.g., "./namd2 +tclsh script.tcl arg1 arg2". |
| 2016/09/18 22:24:32 | jim | +40 -0 | 1.118 | src/ScriptTcl.C | Add --tclmain and +tclsh options to allow passing of command-line arguments to a Tcl script either with (--tclmain) or without (+tclsh) Charm++ startup and NAMD scripting features. E.g., "./namd2 +tclsh script.tcl arg1 arg2". |
| 2016/09/16 18:22:20 | jim | +14 -17 | 1.1262 | src/Molecule.C | From Brian Radak, small fix to LJcorrection calculation. |
| 2016/09/15 20:56:12 | jim | +1 -1 | 1.117 | src/ScriptTcl.C | Return bools to Python from Tcl. |
| 2016/09/15 19:22:21 | jim | +12 -2 | 1.28 | psfgen/src/tcl_psfgen.c | From Brian Radak, add ability to query velocities. |
| 2016/09/15 18:35:37 | jim | +5 -2 | 1.116 | src/ScriptTcl.C | Tcl exit command only initializes if multiple replicas are active. |
| 2016/09/15 17:45:29 | jim | +2 -2 | 1.115 | src/ScriptTcl.C | For Python interface, make tcl.call() and tcl.eval() use the local Tcl context from which python was called rather than the global Tcl context. |
| 2016/09/14 20:22:03 | jim | +16 -0 | 1.1090 | src/Controller.h | From Brian Radak, move TI stdout to separate lines, change PARTITION format in alchOutFile, and other alchemical output fixes. |
| 2016/09/14 20:22:03 | jim | +184 -178 | 1.1321 | src/Controller.C | From Brian Radak, move TI stdout to separate lines, change PARTITION format in alchOutFile, and other alchemical output fixes. |
| 2016/09/14 20:13:26 | jim | +0 -1 | 1.1090 | src/ComputeNonbondedUtil.h | Remove unused static alchLambda. |
| 2016/09/14 20:13:26 | jim | +1 -2 | 1.1123 | src/ComputeNonbondedUtil.C | Remove unused static alchLambda. |
| 2016/09/14 17:10:20 | jim | +16 -0 | 1.114 | src/ScriptTcl.C | Fix Tcl parameter introspection for structure and coordinates. |
| 2016/09/14 17:10:20 | jim | +9 -0 | 1.1011 | src/ConfigList.h | Fix Tcl parameter introspection for structure and coordinates. |
| 2016/09/14 15:47:33 | jim | +4 -0 | 1.1030 | src/main.ci | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:33 | jim | +35 -8 | 1.1289 | src/WorkDistrib.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:33 | jim | +5 -2 | 1.1466 | src/SimParameters.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:33 | jim | None | 1.1 | src/PmeSolverUtil.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:33 | jim | None | 1.1 | src/PmeSolver.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:33 | jim | None | 1.1 | src/PmeSolver.ci | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/PmeSolver.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | +1 -1 | 1.20 | src/PmeKSpace.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | +10 -2 | 1.1071 | src/Patch.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | +56 -7 | 1.1151 | src/Node.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | +8 -0 | 1.1055 | src/NamdTypes.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/DeviceCUDAkernel.cu | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | +33 -4 | 1.4 | src/DeviceCUDA.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | +152 -75 | 1.4 | src/DeviceCUDA.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | +274 -33 | 1.3 | src/CudaUtils.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | +175 -73 | 1.2 | src/CudaUtils.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/CudaTileListKernel.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/CudaTileListKernel.cu | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/CudaPmeSolverUtilKernel.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/CudaPmeSolverUtilKernel.cu | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/CudaPmeSolverUtil.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/CudaPmeSolverUtil.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/CudaPmeSolver.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/CudaPmeSolver.ci | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/CudaPmeSolver.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/CudaComputeNonbondedKernel.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/CudaComputeNonbondedKernel.cu | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/CudaComputeNonbonded.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/CudaComputeNonbonded.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/CudaComputeGBISKernel.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/CudaComputeGBISKernel.cu | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:32 | jim | None | 1.1 | src/ComputePmeCUDAMgr.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | None | 1.1 | src/ComputePmeCUDAMgr.ci | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | None | 1.1 | src/ComputePmeCUDAMgr.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | None | 1.1 | src/ComputePmeCUDA.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | None | 1.1 | src/ComputePmeCUDA.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | +9 -1 | 1.222 | src/ComputePme.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | +3 -1 | 1.1122 | src/ComputeNonbondedUtil.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | +1 -0 | 1.39 | src/ComputeNonbondedCUDAKernel.cu | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | +9 -1 | 1.25 | src/ComputeNonbondedCUDA.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | +23 -26 | 1.101 | src/ComputeNonbondedCUDA.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | +23 -0 | 1.1046 | src/ComputeMgr.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | +14 -0 | 1.1023 | src/ComputeMgr.ci | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | +191 -4 | 1.1130 | src/ComputeMgr.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | +4 -0 | 1.1058 | src/ComputeMap.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | +21 -21 | 1.6 | src/ComputeGBIS.inl | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | None | 1.1 | src/ComputeCUDAMgr.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | None | 1.1 | src/ComputeCUDAMgr.ci | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | None | 1.1 | src/ComputeCUDAMgr.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | +4 -0 | 1.78 | src/BackEnd.C | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:31 | jim | +4 -0 | 1.1033 | src/BOCgroup.h | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:14 | jim | +7 -4 | 1.11 | arch/Win64.cuda | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:14 | jim | +9 -6 | 1.8 | arch/MacOSX-x86_64.cuda | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:14 | jim | +8 -6 | 1.14 | arch/Linux-x86_64.cuda | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:14 | jim | None | 1.1 | arch/Linux-POWER.fftw3 | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:14 | jim | +6 -5 | 1.3 | arch/Linux-POWER.cuda | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:14 | jim | +6 -4 | 1.3 | arch/Linux-ARM64.cuda | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:14 | jim | +6 -4 | 1.5 | arch/Linux-ARM.cuda | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:14 | jim | +5 -3 | 1.7 | arch/CRAY-XT.cuda | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:14 | jim | +5 -3 | 1.5 | arch/CRAY-XE.cuda | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:47:14 | jim | +5 -3 | 1.4 | arch/CRAY-XC.cuda | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:46:49 | jim | +46 -18 | 1.1353 | Makefile | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/14 15:46:48 | jim | +483 -0 | 1.191 | Make.depends | New CUDA kernels and PME from Antti-Pekka Hynninen. Enable with "useCUDA2 yes" and "usePMECUDA yes". |
| 2016/09/13 20:36:25 | jim | +6 -6 | 1.108 | config | Don't confuse CC and CXX environment variables for --cc and --cxx arguments. |
| 2016/09/09 21:10:40 | jim | +2 -0 | 1.54 | src/ComputeNonbondedBase2.h | Disable pragma simd assert for Go forces kernels |
| 2016/09/08 21:12:27 | jim | +1 -1 | 1.2 | arch/Linux-POWER-g++.arch | Use C++ 11 standard. |
| 2016/09/08 21:12:27 | jim | +1 -1 | 1.4 | arch/CRAY-XE-gnu.arch | Use C++ 11 standard. |
| 2016/09/08 21:02:06 | jim | None | 1.1 | cub/cub/warp/specializations/warp_scan_smem.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/warp/specializations/warp_scan_shfl.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/warp/specializations/warp_reduce_smem.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/warp/specializations/warp_reduce_shfl.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/warp/warp_scan.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/warp/warp_reduce.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/thread/thread_store.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/thread/thread_search.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/thread/thread_scan.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/thread/thread_reduce.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/thread/thread_operators.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/thread/thread_load.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/iterator/transform_input_iterator.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/iterator/tex_ref_input_iterator.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/iterator/tex_obj_input_iterator.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/iterator/counting_input_iterator.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/iterator/constant_input_iterator.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/iterator/cache_modified_output_iterator.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/iterator/cache_modified_input_iterator.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/iterator/arg_index_input_iterator.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:05 | jim | None | 1.1 | cub/cub/host/mutex.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:04 | jim | None | 1.1 | cub/cub/grid/grid_queue.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:04 | jim | None | 1.1 | cub/cub/grid/grid_mapping.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:04 | jim | None | 1.1 | cub/cub/grid/grid_even_share.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:04 | jim | None | 1.1 | cub/cub/grid/grid_barrier.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:04 | jim | None | 1.1 | cub/cub/device/dispatch/dispatch_spmv_row_based.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:04 | jim | None | 1.1 | cub/cub/device/dispatch/dispatch_spmv_orig.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:04 | jim | None | 1.1 | cub/cub/device/dispatch/dispatch_spmv_csrt.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:04 | jim | None | 1.1 | cub/cub/device/dispatch/dispatch_select_if.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:04 | jim | None | 1.1 | cub/cub/device/dispatch/dispatch_scan.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:04 | jim | None | 1.1 | cub/cub/device/dispatch/dispatch_rle.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:04 | jim | None | 1.1 | cub/cub/device/dispatch/dispatch_reduce_by_key.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:04 | jim | None | 1.1 | cub/cub/device/dispatch/dispatch_reduce.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:04 | jim | None | 1.1 | cub/cub/device/dispatch/dispatch_radix_sort.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:04 | jim | None | 1.1 | cub/cub/device/dispatch/dispatch_histogram.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:04 | jim | None | 1.1 | cub/cub/device/device_spmv.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:04 | jim | None | 1.1 | cub/cub/device/device_select.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:03 | jim | None | 1.1 | cub/cub/device/device_segmented_reduce.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:03 | jim | None | 1.1 | cub/cub/device/device_segmented_radix_sort.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:03 | jim | None | 1.1 | cub/cub/device/device_scan.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:03 | jim | None | 1.1 | cub/cub/device/device_run_length_encode.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:03 | jim | None | 1.1 | cub/cub/device/device_reduce.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:03 | jim | None | 1.1 | cub/cub/device/device_radix_sort.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:03 | jim | None | 1.1 | cub/cub/device/device_partition.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:03 | jim | None | 1.1 | cub/cub/device/device_histogram.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:03 | jim | None | 1.1 | cub/cub/block/specializations/block_scan_warp_scans.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:03 | jim | None | 1.1 | cub/cub/block/specializations/block_scan_raking.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:03 | jim | None | 1.1 | cub/cub/block/specializations/block_reduce_warp_reductions.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:03 | jim | None | 1.1 | cub/cub/block/specializations/block_reduce_raking_commutative_only.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:03 | jim | None | 1.1 | cub/cub/block/specializations/block_reduce_raking.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:03 | jim | None | 1.1 | cub/cub/block/specializations/block_histogram_sort.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/block/specializations/block_histogram_atomic.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/block/block_store.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/block/block_shuffle.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/block/block_scan.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/block/block_reduce_by_key.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/block/block_reduce.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/block/block_raking_layout.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/block/block_radix_sort.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/block/block_radix_rank.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/block/block_load.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/block/block_histogram.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/block/block_exchange.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/block/block_discontinuity.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/agent/single_pass_scan_operators.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/agent/agent_spmv_row_based.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/agent/agent_spmv_orig.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/agent/agent_spmv_csrt.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:02 | jim | None | 1.1 | cub/cub/agent/agent_select_if.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/agent/agent_segment_fixup.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/agent/agent_scan.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/agent/agent_rle.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/agent/agent_reduce_by_key.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/agent/agent_reduce.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/agent/agent_radix_sort_upsweep.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/agent/agent_radix_sort_downsweep.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/agent/agent_histogram.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/util_type.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/util_ptx.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/util_namespace.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/util_macro.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/util_device.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/util_debug.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/util_arch.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/util_allocator.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:02:01 | jim | None | 1.1 | cub/cub/cub.cuh | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:01:51 | jim | None | 1.1 | cub/LICENSE.TXT | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 21:01:50 | jim | None | 1.1 | cub/CHANGE_LOG.TXT | Add CUB 1.5.2 library of CUDA primitives. |
| 2016/09/08 19:35:05 | jim | +4 -0 | 1.5 | src/ComputeNonbondedBase2KNL.h | Work around segfault in Intel 2017 compiler (the compiler itself segfaults). |
| 2016/09/07 20:54:04 | jim | +7 -0 | 1.1236 | src/HomePatch.C | Regenerate rattle list etc. after checkpoint load or atom exchange. |
| 2016/09/07 18:09:59 | jim | +5 -6 | 1.1288 | src/WorkDistrib.C | From Brian Radak, alchemical cleanup and disable/re-enable alch in script. |
| 2016/09/07 18:09:59 | jim | +3 -2 | 1.1243 | src/SimParameters.h | From Brian Radak, alchemical cleanup and disable/re-enable alch in script. |
| 2016/09/07 18:09:59 | jim | +14 -9 | 1.1465 | src/SimParameters.C | From Brian Radak, alchemical cleanup and disable/re-enable alch in script. |
| 2016/09/07 18:09:59 | jim | +2 -2 | 1.1089 | src/NamdState.C | From Brian Radak, alchemical cleanup and disable/re-enable alch in script. |
| 2016/09/07 18:09:59 | jim | +113 -115 | 1.1261 | src/Molecule.C | From Brian Radak, alchemical cleanup and disable/re-enable alch in script. |
| 2016/09/07 18:09:59 | jim | +1 -1 | 1.36 | src/ComputePme.h | From Brian Radak, alchemical cleanup and disable/re-enable alch in script. |
| 2016/09/07 18:09:58 | jim | +14 -14 | 1.221 | src/ComputePme.C | From Brian Radak, alchemical cleanup and disable/re-enable alch in script. |
| 2016/09/06 19:50:46 | jim | +1 -0 | 1.1150 | src/Node.C | Rebuild CUDA exclusion list after reloading structure. |
| 2016/09/06 19:50:46 | jim | +15 -4 | 1.38 | src/ComputeNonbondedCUDAKernel.cu | Rebuild CUDA exclusion list after reloading structure. |
| 2016/09/06 19:50:46 | jim | +1 -1 | 1.24 | src/ComputeNonbondedCUDA.h | Rebuild CUDA exclusion list after reloading structure. |
| 2016/09/06 19:50:46 | jim | +6 -0 | 1.100 | src/ComputeNonbondedCUDA.C | Rebuild CUDA exclusion list after reloading structure. |
| 2016/09/06 19:50:45 | jim | +2 -0 | 1.1045 | src/ComputeMgr.h | Rebuild CUDA exclusion list after reloading structure. |
| 2016/09/06 19:50:45 | jim | +1 -0 | 1.1022 | src/ComputeMgr.ci | Rebuild CUDA exclusion list after reloading structure. |
| 2016/09/06 19:50:45 | jim | +19 -0 | 1.1129 | src/ComputeMgr.C | Rebuild CUDA exclusion list after reloading structure. |
| 2016/09/06 18:17:54 | jim | +1 -3 | 1.1235 | src/HomePatch.C | Tweak rattle list regeneration flag. |
| 2016/09/06 17:58:39 | jim | +2 -0 | 1.1089 | src/HomePatch.h | Fix bond checksum error after reinitatoms with single-patch non-periodic simulation. |
| 2016/09/06 17:58:38 | jim | +11 -3 | 1.1234 | src/HomePatch.C | Fix bond checksum error after reinitatoms with single-patch non-periodic simulation. |
| 2016/09/05 18:25:43 | jim | +3 -7 | 1.1242 | src/SimParameters.h | Alchemical cleanup from Brian Radak. |
| 2016/09/05 18:25:43 | jim | +126 -166 | 1.1464 | src/SimParameters.C | Alchemical cleanup from Brian Radak. |
| 2016/09/05 18:25:42 | jim | +1 -1 | 1.113 | src/ScriptTcl.C | Alchemical cleanup from Brian Radak. |
| 2016/09/05 18:25:42 | jim | +2 -3 | 1.1320 | src/Controller.C | Alchemical cleanup from Brian Radak. |
| 2016/09/05 17:57:36 | jim | +1 -0 | 1.190 | Make.depends | Update dependencies for aggregate virial calculation. |
| 2016/09/04 11:07:24 | jim | +6 -2 | 1.25 | src/PatchTypes.h | Eliminate aggregate virial calculation overhead for CUDA builds. |
| 2016/09/04 11:07:23 | jim | +6 -0 | 1.1070 | src/Patch.C | Eliminate aggregate virial calculation overhead for CUDA builds. |
| 2016/09/04 11:07:22 | jim | +4 -0 | 1.1063 | src/ComputeNonbondedSelf.C | Eliminate aggregate virial calculation overhead for CUDA builds. |
| 2016/09/04 11:07:22 | jim | +4 -0 | 1.1070 | src/ComputeNonbondedPair.C | Eliminate aggregate virial calculation overhead for CUDA builds. |
| 2016/09/03 19:13:05 | jim | +34 -13 | 1.107 | config | Add support for spaces in cuda-prefix on Windows and cufft library. |
| 2016/08/29 22:15:46 | jim | +1 -1 | 1.24 | src/PatchTypes.h | Switch virial calculation to use aggregate rather than pairwise forces. |
| 2016/08/29 22:15:46 | jim | +3 -1 | 1.1047 | src/Patch.h | Switch virial calculation to use aggregate rather than pairwise forces. |
| 2016/08/29 22:15:46 | jim | +54 -0 | 1.1069 | src/Patch.C | Switch virial calculation to use aggregate rather than pairwise forces. |
| 2016/08/29 22:15:46 | jim | +4 -4 | 1.1062 | src/ComputeNonbondedSelf.C | Switch virial calculation to use aggregate rather than pairwise forces. |
| 2016/08/29 22:15:46 | jim | +4 -4 | 1.1069 | src/ComputeNonbondedPair.C | Switch virial calculation to use aggregate rather than pairwise forces. |
| 2016/08/29 22:15:46 | jim | +8 -21 | 1.4 | src/ComputeNonbondedBase2KNL.h | Switch virial calculation to use aggregate rather than pairwise forces. |
| 2016/08/29 22:15:45 | jim | +2 -31 | 1.53 | src/ComputeNonbondedBase2.h | Switch virial calculation to use aggregate rather than pairwise forces. |
| 2016/08/29 22:15:45 | jim | +47 -127 | 1.1190 | src/ComputeNonbondedBase.h | Switch virial calculation to use aggregate rather than pairwise forces. |
| 2016/08/29 22:11:58 | jim | +1 -1 | 1.1089 | src/ComputeNonbondedUtil.h | Tweak KNL interpolation table size to have grid point at 8/10/12 A cutoff distances. |
| 2016/08/29 04:40:09 | jim | +4 -4 | 1.3 | src/ComputeNonbondedBase2KNL.h | Fix KNL kernel for PME without multiple timestepping. |
| 2016/08/26 19:40:33 | jim | +3 -2 | 1.1063 | src/Sequencer.h | Integrator cleanup from Brian Radak. |
| 2016/08/26 19:40:32 | jim | +39 -71 | 1.1230 | src/Sequencer.C | Integrator cleanup from Brian Radak. |
| 2016/08/26 17:39:59 | jim | +2 -0 | 1.2 | arch/Linux-x86_64.mkl | MKL static link options. Commented out because needs new charmc that avoid reordering arguments. |
| 2016/08/26 17:09:26 | jim | +1 -1 | 1.2 | arch/Linux-KNL-icc.arch | Generate optimization reports. |
| 2016/08/26 16:18:44 | jim | +2 -0 | 1.1068 | src/Patch.C | Eliminate emulated gather by storing vdwType as int. |
| 2016/08/26 16:18:43 | jim | +1 -6 | 1.1054 | src/NamdTypes.h | Eliminate emulated gather by storing vdwType as int. |
| 2016/08/26 16:18:42 | jim | +2 -1 | 1.2 | src/ComputeNonbondedBase2KNL.h | Eliminate emulated gather by storing vdwType as int. |
| 2016/08/23 21:29:08 | jim | +6 -0 | 1.1046 | src/Patch.h | Optimized kernel for KNL. |
| 2016/08/23 21:29:08 | jim | +19 -0 | 1.1067 | src/Patch.C | Optimized kernel for KNL. |
| 2016/08/23 21:29:08 | jim | +15 -0 | 1.1053 | src/NamdTypes.h | Optimized kernel for KNL. |
| 2016/08/23 21:29:08 | jim | +4 -0 | 1.1012 | src/LJTable.h | Optimized kernel for KNL. |
| 2016/08/23 21:29:08 | jim | +39 -2 | 1.1088 | src/ComputeNonbondedUtil.h | Optimized kernel for KNL. |
| 2016/08/23 21:29:08 | jim | +106 -8 | 1.1121 | src/ComputeNonbondedUtil.C | Optimized kernel for KNL. |
| 2016/08/23 21:29:08 | jim | +6 -0 | 1.1061 | src/ComputeNonbondedSelf.C | Optimized kernel for KNL. |
| 2016/08/23 21:29:08 | jim | +9 -28 | 1.1068 | src/ComputeNonbondedPair.C | Optimized kernel for KNL. |
| 2016/08/23 21:29:08 | jim | +77 -2 | 1.16 | src/ComputeNonbondedInl.h | Optimized kernel for KNL. |
| 2016/08/23 21:29:08 | jim | None | 1.1 | src/ComputeNonbondedBase2KNL.h | Optimized kernel for KNL. |
| 2016/08/23 21:29:08 | jim | +85 -3 | 1.1189 | src/ComputeNonbondedBase.h | Optimized kernel for KNL. |
| 2016/08/23 21:29:00 | jim | +7 -0 | 1.189 | Make.depends | Optimized kernel for KNL. |
| 2016/08/22 16:26:56 | jim | +1 -0 | 1.39 | src/ComputePmeMgr.ci | Enable vectorization of recv_grid. |
| 2016/08/22 16:26:55 | jim | +15 -4 | 1.220 | src/ComputePme.C | Enable vectorization of recv_grid. |
| 2016/08/22 16:16:02 | jim | +4 -4 | 1.26 | src/ResizeArrayRaw.h | Align data to 64-byte boundaries. |
| 2016/08/16 23:51:38 | jim | +2 -0 | 1.2 | lib/replica/umbrella_mplex.namd | Fix bugs that ignored input_root and first_timestep. |
| 2016/08/16 23:51:38 | jim | +1 -0 | 1.3 | lib/replica/multiplex.namd | Fix bugs that ignored input_root and first_timestep. |
| 2016/08/14 21:04:46 | jim | None | 1.1 | arch/CRAY-XC-KNL.tcl | Add Cray XC KNL arch files. |
| 2016/08/14 21:04:46 | jim | None | 1.1 | arch/CRAY-XC-KNL.fftw3 | Add Cray XC KNL arch files. |
| 2016/08/14 21:04:46 | jim | None | 1.1 | arch/CRAY-XC-KNL.fftw | Add Cray XC KNL arch files. |
| 2016/08/14 21:04:46 | jim | None | 1.1 | arch/CRAY-XC-KNL.base | Add Cray XC KNL arch files. |
| 2016/08/14 21:04:46 | jim | None | 1.1 | arch/CRAY-XC-KNL-intel.arch | Add Cray XC KNL arch files. |
| 2016/08/09 21:51:30 | jim | +4 -0 | 1.1060 | src/common.C | Print "(unknown error)" rather than segfault if null is passed to NAMD_die variants. |
| 2016/08/09 21:43:25 | jim | +3 -3 | 1.112 | src/ScriptTcl.C | Pass "Unknown Tcl error" to NAMD_die rather than null if errorInfo is unset. |
| 2016/08/09 21:43:24 | jim | +2 -2 | 1.24 | src/GlobalMasterTcl.C | Pass "Unknown Tcl error" to NAMD_die rather than null if errorInfo is unset. |
| 2016/08/09 21:43:24 | jim | +2 -2 | 1.9 | src/ComputeTclBC.C | Pass "Unknown Tcl error" to NAMD_die rather than null if errorInfo is unset. |
| 2016/07/29 21:16:22 | jim | +9 -9 | 1.1463 | src/SimParameters.C | Add config options for Intel Math Kernel Library. |
| 2016/07/29 21:16:20 | jim | None | 1.1 | arch/Linux-x86_64.mkl | Add config options for Intel Math Kernel Library. |
| 2016/07/29 21:16:20 | jim | None | 1.1 | arch/Linux-KNL.mkl | Add config options for Intel Math Kernel Library. |
| 2016/07/29 21:16:16 | jim | +30 -2 | 1.106 | config | Add config options for Intel Math Kernel Library. |
| 2016/07/28 15:24:38 | jim | None | 1.1 | arch/Linux-KNL.tcl | Add arch files for Intel Xeon Phi KNL processor (self-hosted, not co-processor). |
| 2016/07/28 15:24:38 | jim | None | 1.1 | arch/Linux-KNL.fftw3 | Add arch files for Intel Xeon Phi KNL processor (self-hosted, not co-processor). |
| 2016/07/28 15:24:38 | jim | None | 1.1 | arch/Linux-KNL.fftw | Add arch files for Intel Xeon Phi KNL processor (self-hosted, not co-processor). |
| 2016/07/28 15:24:38 | jim | None | 1.1 | arch/Linux-KNL.base | Add arch files for Intel Xeon Phi KNL processor (self-hosted, not co-processor). |
| 2016/07/28 15:24:38 | jim | None | 1.1 | arch/Linux-KNL-icc.arch | Add arch files for Intel Xeon Phi KNL processor (self-hosted, not co-processor). |
| 2016/07/28 15:24:33 | jim | +4 -0 | 1.105 | config | Add arch files for Intel Xeon Phi KNL processor (self-hosted, not co-processor). |
| 2016/07/21 20:33:30 | jim | +1 -0 | 1.1006 | src/dc.pl | Add obj/.exists dependencies to all targets in obj directory. |
| 2016/07/21 20:33:26 | jim | +211 -0 | 1.188 | Make.depends | Add obj/.exists dependencies to all targets in obj directory. |
| 2016/06/30 18:47:37 | jim | +1 -1 | 1.69 | ug/Makefile | Work around unusual sh echo behavior on Ubuntu when creating namd_version.tex. |
| 2016/06/29 21:30:01 | jim | +19 -6 | 1.27 | psfgen/src/tcl_psfgen.c | From Brian Radak, new "segment mass" psfgen command. |
| 2016/06/29 21:26:26 | jim | +33 -1 | 1.33 | ug/ug_alchemy.tex | From Brian Radak, alchemy doc updates. |
| 2016/06/29 21:25:17 | jim | +2 -2 | 1.23 | ug/ug_forcefield.tex | From Brian Radak, remove LJcorrection/vdwForceSwitching warning. |
| 2016/06/20 22:21:01 | jim | +20 -2 | 1.111 | src/ScriptTcl.C | Improve typing of values returned from Tcl to Python. |
| 2016/06/20 21:19:21 | jim | +4 -4 | 1.110 | src/ScriptTcl.C | Hide Python helper classes with leading underscore. |
| 2016/06/13 20:11:30 | jim | +1 -1 | 1.109 | src/ScriptTcl.C | Run until numsteps if run/minimize were never called, even if initialization was triggered. |
| 2016/06/08 22:06:21 | jim | +2 -5 | 1.1089 | src/Controller.h | Bug fix from Brian Radak for alchFep bonded energy forward displacement in alchLambda, also only record alchemical energy differences and other cleanups. |
| 2016/06/08 22:06:21 | jim | +94 -96 | 1.1319 | src/Controller.C | Bug fix from Brian Radak for alchFep bonded energy forward displacement in alchLambda, also only record alchemical energy differences and other cleanups. |
| 2016/06/08 22:06:21 | jim | +4 -3 | 1.1035 | src/ComputeImpropers.C | Bug fix from Brian Radak for alchFep bonded energy forward displacement in alchLambda, also only record alchemical energy differences and other cleanups. |
| 2016/06/08 22:06:21 | jim | +2 -3 | 1.1038 | src/ComputeDihedrals.C | Bug fix from Brian Radak for alchFep bonded energy forward displacement in alchLambda, also only record alchemical energy differences and other cleanups. |
| 2016/06/08 22:06:21 | jim | +2 -3 | 1.1035 | src/ComputeBonds.C | Bug fix from Brian Radak for alchFep bonded energy forward displacement in alchLambda, also only record alchemical energy differences and other cleanups. |
| 2016/06/08 22:06:20 | jim | +2 -3 | 1.1038 | src/ComputeAngles.C | Bug fix from Brian Radak for alchFep bonded energy forward displacement in alchLambda, also only record alchemical energy differences and other cleanups. |
