#include "InfoStream.h"
#include "BackEnd.h"
#include "ScriptTcl.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 <errno.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"

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

#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 562 of file ScriptTcl.C.

#define DEG2RAD 3.14159625359/180.0

Definition at line 1761 of file ScriptTcl.C.

Referenced by get_lattice_from_ts().

#define MIN_DEBUG_LEVEL 4

Definition at line 49 of file ScriptTcl.C.

#define UNITCELLSLOP 0.0001

Definition at line 1762 of file ScriptTcl.C.

Function Documentation

static int atoBool ( const char * s )

static

Definition at line 967 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;
 }

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}");
 }

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

static

Definition at line 1764 of file ScriptTcl.C.

References A, B, 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;
 }

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

Definition at line 2088 of file ScriptTcl.C.

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

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

Definition at line 2092 of file ScriptTcl.C.

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

int psfgen_static_init ( Tcl_Interp * )

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

void read_binary_coors	(	char *	fname,
		PDB *	pdbobj
	)

Definition at line 34 of file NamdOneTools.C.

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

Referenced by NamdState::loadStructure().

                                                  {
   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()

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

static

Definition at line 56 of file ScriptTcl.C.

References dcdplugin.

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

static int replica_hash ( const char * key )

static

Definition at line 1581 of file ScriptTcl.C.

                                          {
   unsigned int hash = 0;
 
   while (*key) {
     hash *= 73;
     hash += *key++;
   }
 
   return hash % CmiNumPartitions();
 }

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

Variable Documentation

float* coords

static

Definition at line 66 of file ScriptTcl.C.

Referenced by Tcl_loadCoords().

molfile_plugin_t* dcdplugin

static

Definition at line 55 of file ScriptTcl.C.

Referenced by register_cb().

void* filehandle

static

Definition at line 65 of file ScriptTcl.C.

int numatoms

static

Definition at line 64 of file ScriptTcl.C.

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

Vector* vcoords

static

Definition at line 67 of file ScriptTcl.C.

Macros

Functions

Variables

Macro Definition Documentation

Function Documentation

Variable Documentation