ScriptTcl.C File Reference

#include "InfoStream.h"
#include "BackEnd.h"
#include "ScriptTcl.h"
#include "converse.h"
#include "Broadcasts.h"
#include "ConfigList.h"
#include "Node.h"
#include "PDB.h"
#include "WorkDistrib.h"
#include "NamdState.h"
#include "Output.h"
#include "Controller.h"
#include "SimParameters.h"
#include "Thread.h"
#include "ProcessorPrivate.h"
#include "PatchMgr.h"
#include "PatchMap.h"
#include "Measure.h"
#include "colvarmodule.h"
#include "colvarscript.h"
#include "DumpBench.h"
#include "ComputeMgr.h"
#include <stdio.h>
#include <ctype.h>
#include <strings.h>
#include "qd.h"
#include <tcl.h>
#include "TclCommands.h"
#include "DataExchanger.h"
#include "Debug.h"
#include "molfile_plugin.h"
#include "libmolfile_plugin.h"
#include "ComputeConsForceMsgs.h"

Go to the source code of this file.

Classes
struct	ScriptTcl::SimpleBroadcastObjectWrapper

Macros
#define	MIN_DEBUG_LEVEL   4
#define	CHECK_REPLICA(REP)
#define	DEG2RAD   3.14159625359/180.0
#define	UNITCELLSLOP   0.0001

Functions
static int	register_cb (void *v, vmdplugin_t *p)
static int	atoBool (const char *s)
int	tcl_run_colvarscript_command (ClientData clientData, Tcl_Interp *interp_in, int objc, Tcl_Obj *const objv[])
static int	replica_hash (const char *key)
void	read_binary_coors (char *fname, PDB *pdbobj)
static int	get_lattice_from_ts (Lattice *lattice, const molfile_timestep_t *ts)
void	newhandle_msg (void *vdata, void *v, const char *msg)
void	newhandle_msg_ex (void *vdata, void *v, const char *msg, int prepend, int newline)
int	psfgen_static_init (Tcl_Interp *)
int	eabf_static_init (Tcl_Interp *)

Variables
static molfile_plugin_t *	dcdplugin
static int	numatoms
static void *	filehandle
static float *	coords
static Vector *	vcoords

Macro Definition Documentation

CHECK_REPLICA

#define CHECK_REPLICA

(

REP

)

Value:

do {\
  if ( (REP) < 0 ) { \
    Tcl_SetResult(interp,(char*)"negative replica index",TCL_VOLATILE); \
    return TCL_ERROR; \
  } \
  if ( (REP) >= CmiNumPartitions() ) { \
    Tcl_SetResult(interp,(char*)"non-existent replica index",TCL_VOLATILE); \
    return TCL_ERROR; \
  } \
} while ( 0 )

Definition at line 567 of file ScriptTcl.C.

DEG2RAD

#define DEG2RAD   3.14159625359/180.0

Definition at line 1802 of file ScriptTcl.C.

Referenced by get_lattice_from_ts().

MIN_DEBUG_LEVEL

#define MIN_DEBUG_LEVEL   4

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 50 of file ScriptTcl.C.

UNITCELLSLOP

#define UNITCELLSLOP   0.0001

Definition at line 1803 of file ScriptTcl.C.

Function Documentation

atoBool()

static int atoBool ( const char *  s )

static

Definition at line 972 of file ScriptTcl.C.

{
   if (!strcasecmp(s, "on")) return 1;
   if (!strcasecmp(s, "off")) return 0;
   if (!strcasecmp(s, "true")) return 1;
   if (!strcasecmp(s, "false")) return 0;
   if (!strcasecmp(s, "yes")) return 1;
   if (!strcasecmp(s, "no")) return 0;
   if (!strcasecmp(s, "1")) return 1;
   if (!strcasecmp(s, "0")) return 0;
   return -1;
}

eabf_static_init()

int eabf_static_init

(

Tcl_Interp *

)

Definition at line 179 of file eabfTcl.C.

References Eabf_Init().

Referenced by ScriptTcl::ScriptTcl(), and ScriptTcl::tclsh().

                                         {
  Tcl_StaticPackage(0,"Eabf",Eabf_Init,0);
  return Tcl_Eval(interp,"package ifneeded Eabf 1.0.0 {load {} Eabf}");
}

get_lattice_from_ts()

static int get_lattice_from_ts ( Lattice *  lattice, const molfile_timestep_t *  ts  )

static

Definition at line 1805 of file ScriptTcl.C.

References DEG2RAD, Lattice::set(), Vector::x, Vector::y, and Vector::z.

{
  // Check if valid unit cell data is contained in the timestep.  We don't
  // have any formalized way of doing this yet; for now, just check that
  // the length of the vector is greater than 1.
  if (ts->A <= 1 || ts->B <= 1 || ts->C <= 1) return 0;

  // convert from degrees to radians
  // Try to get exact results when the angles are exactly 90.
  double epsalpha = DEG2RAD*(ts->alpha-90.0);
  double epsbeta  = DEG2RAD*(ts->beta-90.0);
  double epsgamma = DEG2RAD*(ts->gamma-90.0);
  double cosAB = -sin(epsgamma);
  double sinAB = cos(epsgamma);
  double cosAC = -sin(epsbeta);
  double cosBC = -sin(epsalpha);

  // A will lie along the positive x axis.
  // B will lie in the x-y plane
  // The origin will be (0,0,0).
  Vector A(0), B(0), vecC(0);
  A.x = ts->A;
  B.x = ts->B*cosAB;
  B.y = ts->B*sinAB;
  //if (fabs(B.x) < UNITCELLSLOP) B.x = 0;
  //if (fabs(B.y) < UNITCELLSLOP) B.y = 0;
  vecC.x = ts->C * cosAC;
  vecC.y = (ts->B*ts->C*cosBC - B.x*vecC.x)/B.y;
  vecC.z = sqrt(ts->C*ts->C - vecC.x*vecC.x - vecC.y*vecC.y);
  //if (fabs(vecC.x) < UNITCELLSLOP) vecC.x = 0;
  //if (fabs(vecC.y) < UNITCELLSLOP) vecC.y = 0;
  //if (fabs(vecC.z) < UNITCELLSLOP) vecC.z = 0;
  lattice->set(A, B, vecC, Vector(0));
  return 1;
}

newhandle_msg()

void newhandle_msg	(	void *	vdata,
		void *	v,
		const char *	msg
	)

Definition at line 2197 of file ScriptTcl.C.

                                                                     {
  CkPrintf("psfgen) %s\n",msg);
}

newhandle_msg_ex()

void newhandle_msg_ex	(	void *	vdata,
		void *	v,
		const char *	msg,
		int	prepend,
		int	newline
	)

Definition at line 2201 of file ScriptTcl.C.

                                                                                                  {
  CkPrintf("%s%s%s", (prepend ? "psfgen) " : ""), msg, (newline ? "\n" : ""));
}

psfgen_static_init()

int psfgen_static_init

(

Tcl_Interp *

)

Referenced by ScriptTcl::ScriptTcl(), and ScriptTcl::tclsh().

read_binary_coors()

void read_binary_coors	(	char *	fname,
		PDB *	pdbobj
	)

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 34 of file NamdOneTools.C.

References PDB::num_atoms(), read_binary_file(), and PDB::set_all_positions().

                                                 {
  Vector *newcoords;    //  Array of vectors to hold coordinates from file

  //  Allocate an array to hold the new coordinates
  newcoords = new Vector[pdbobj->num_atoms()];

  //  Read the coordinate from the file
  read_binary_file(fname,newcoords,pdbobj->num_atoms());

  //  Set the coordinates in the PDB object to the new coordinates
  pdbobj->set_all_positions(newcoords);

  //  Clean up
  delete [] newcoords;

} // END OF FUNCTION read_binary_coors()

register_cb()

static int register_cb ( void *  v, vmdplugin_t *  p  )

static

Definition at line 57 of file ScriptTcl.C.

References dcdplugin.

Referenced by ScriptTcl::ScriptTcl().

                                                {
        dcdplugin = (molfile_plugin_t *)p;
        return 0;
}

replica_hash()

static int replica_hash ( const char *  key )

static

Definition at line 1594 of file ScriptTcl.C.

                                         {
  unsigned int hash = 0;

  while (*key) {
    hash *= 73;
    hash += *key++;
  }

  return hash % CmiNumPartitions();
}

tcl_run_colvarscript_command()

int tcl_run_colvarscript_command	(	ClientData	clientData,
		Tcl_Interp *	interp_in,
		int	objc,
		Tcl_Obj *const	objv[]
	)

Variable Documentation

coords

float* coords

static

Definition at line 67 of file ScriptTcl.C.

Referenced by IMDOutput::gather_coordinates(), imd_recv_fcoords(), imd_send_fcoords(), GlobalMasterIMD::send_fcoords(), and Tcl_loadCoords().

dcdplugin

molfile_plugin_t* dcdplugin

static

Definition at line 56 of file ScriptTcl.C.

Referenced by register_cb().

filehandle

void* filehandle

static

Definition at line 66 of file ScriptTcl.C.

numatoms

int numatoms

static

Definition at line 65 of file ScriptTcl.C.

Referenced by NamdState::loadStructure(), rescale_nonperiodic_cell(), and spatial_hashing().

vcoords

Vector* vcoords

static

Definition at line 68 of file ScriptTcl.C.