NAMD
Macros | Functions | Variables
ScriptTcl.C File Reference
#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"

Go to the source code of this file.

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 *v, const char *msg)
 
void newhandle_msg_ex (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 voidfilehandle
 
static float * coords
 
static Vectorvcoords
 

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 )
if(ComputeNonbondedUtil::goMethod==2)

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

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

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.

968 {
969  if (!strcasecmp(s, "on")) return 1;
970  if (!strcasecmp(s, "off")) return 0;
971  if (!strcasecmp(s, "true")) return 1;
972  if (!strcasecmp(s, "false")) return 0;
973  if (!strcasecmp(s, "yes")) return 1;
974  if (!strcasecmp(s, "no")) return 0;
975  if (!strcasecmp(s, "1")) return 1;
976  if (!strcasecmp(s, "0")) return 0;
977  return -1;
978 }
int eabf_static_init ( Tcl_Interp *  )

Definition at line 179 of file eabfTcl.C.

References Eabf_Init().

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

179  {
180  Tcl_StaticPackage(0,"Eabf",Eabf_Init,0);
181  return Tcl_Eval(interp,"package ifneeded Eabf 1.0.0 {load {} Eabf}");
182 }
int Eabf_Init(Tcl_Interp *stupidTcl)
Definition: eabfTcl.C:165
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.

1765 {
1766  // Check if valid unit cell data is contained in the timestep. We don't
1767  // have any formalized way of doing this yet; for now, just check that
1768  // the length of the vector is greater than 1.
1769  if (ts->A <= 1 || ts->B <= 1 || ts->C <= 1) return 0;
1770 
1771  // convert from degrees to radians
1772  // Try to get exact results when the angles are exactly 90.
1773  double epsalpha = DEG2RAD*(ts->alpha-90.0);
1774  double epsbeta = DEG2RAD*(ts->beta-90.0);
1775  double epsgamma = DEG2RAD*(ts->gamma-90.0);
1776  double cosAB = -sin(epsgamma);
1777  double sinAB = cos(epsgamma);
1778  double cosAC = -sin(epsbeta);
1779  double cosBC = -sin(epsalpha);
1780 
1781  // A will lie along the positive x axis.
1782  // B will lie in the x-y plane
1783  // The origin will be (0,0,0).
1784  Vector A(0), B(0), vecC(0);
1785  A.x = ts->A;
1786  B.x = ts->B*cosAB;
1787  B.y = ts->B*sinAB;
1788  //if (fabs(B.x) < UNITCELLSLOP) B.x = 0;
1789  //if (fabs(B.y) < UNITCELLSLOP) B.y = 0;
1790  vecC.x = ts->C * cosAC;
1791  vecC.y = (ts->B*ts->C*cosBC - B.x*vecC.x)/B.y;
1792  vecC.z = sqrt(ts->C*ts->C - vecC.x*vecC.x - vecC.y*vecC.y);
1793  //if (fabs(vecC.x) < UNITCELLSLOP) vecC.x = 0;
1794  //if (fabs(vecC.y) < UNITCELLSLOP) vecC.y = 0;
1795  //if (fabs(vecC.z) < UNITCELLSLOP) vecC.z = 0;
1796  lattice->set(A, B, vecC, Vector(0));
1797  return 1;
1798 }
#define DEG2RAD
Definition: ScriptTcl.C:1761
const BigReal A
Definition: Vector.h:64
void set(Vector A, Vector B, Vector C)
Definition: Lattice.h:31
const BigReal B
void newhandle_msg ( void v,
const char *  msg 
)

Definition at line 2088 of file ScriptTcl.C.

2088  {
2089  CkPrintf("psfgen) %s\n",msg);
2090 }
void newhandle_msg_ex ( void v,
const char *  msg,
int  prepend,
int  newline 
)

Definition at line 2092 of file ScriptTcl.C.

2092  {
2093  CkPrintf("%s%s%s", (prepend ? "psfgen) " : ""), msg, (newline ? "\n" : ""));
2094 }
int psfgen_static_init ( Tcl_Interp *  )
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().

Referenced by NamdState::loadStructure().

34  {
35  Vector *newcoords; // Array of vectors to hold coordinates from file
36 
37  // Allocate an array to hold the new coordinates
38  newcoords = new Vector[pdbobj->num_atoms()];
39 
40  // Read the coordinate from the file
41  read_binary_file(fname,newcoords,pdbobj->num_atoms());
42 
43  // Set the coordinates in the PDB object to the new coordinates
44  pdbobj->set_all_positions(newcoords);
45 
46  // Clean up
47  delete [] newcoords;
48 
49 } // END OF FUNCTION read_binary_coors()
Definition: Vector.h:64
void set_all_positions(Vector *)
Definition: PDB.C:331
int num_atoms(void)
Definition: PDB.C:323
void read_binary_file(const char *fname, Vector *data, int n)
Definition: NamdOneTools.C:52
static int register_cb ( void v,
vmdplugin_t *  p 
)
static

Definition at line 56 of file ScriptTcl.C.

References dcdplugin.

56  {
57  dcdplugin = (molfile_plugin_t *)p;
58  return 0;
59 }
static molfile_plugin_t * dcdplugin
Definition: ScriptTcl.C:55
static int replica_hash ( const char *  key)
static

Definition at line 1581 of file ScriptTcl.C.

1581  {
1582  unsigned int hash = 0;
1583 
1584  while (*key) {
1585  hash *= 73;
1586  hash += *key++;
1587  }
1588 
1589  return hash % CmiNumPartitions();
1590 }
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.