[gvd-devel] GVD dies upon opening source file

Maura Edelweiss memonvil@artsci.wustl.edu
Sun, 27 Jan 2002 00:17:45 -0600
Previous message: [gvd-devel] Advertise with E-Mail Marketing!
Next message: [gvd-devel] GVD dies upon opening source file
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
This is a multi-part message in MIME format.
--------------F619EEC86E7557089097B822
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Please, find attached my source C code and the GCD log file.
I simply edited my file off-line using "vi". I recreated the executable
code and start GVD again.
Upon opening the source code a message popped up requesting a bug
report. At this point GVD died when I selected "OK"
I restarted GVD again three times and repeated the same operations and
its behaviour was consistent.

Question:  GVD allows for on-line source editing. Does it automatically
recreates the executable code  upon saving the 
           buffer containing the modifications ???

Regards,
Maura E.M.
--------------F619EEC86E7557089097B822
Content-Type: text/plain; charset=us-ascii;
 name="mdJan21.02.c"
Content-Transfer-Encoding: 7bit
Content-Disposition: inline;
 filename="mdJan21.02.c"

/***************************************************************************/
/*                          mdJan21.02.c                                   */
/*********               MOLECULAR SIMULATION  ... redo           **********/
/*                             -------------------                         */
/*    begin                : Mon Jan 21 2002                               */
/*    copyright            : (C) 2002 by  Maura Edelweiss Monville         */
/*    email                :                                               */
/***************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <malloc.h>
#include <unistd.h>

/* position, velocities, forces components       */
double *X;     /* Record x-coordinate            */
double *Y;     /* Record y-coordinate            */
double *Z;     /* Record z-coordinate            */
double *Vx;    /* velocity x-coordinate          */
double *Vy;    /* velocity y-coordinate          */
double *Vz;    /* velocity z-coordinate          */
double *Fx;    /* cumulative force x-coordinate  */
double *Fy;    /* cumulative force y-coordinate  */
double *Fz;    /* cumulative force z-coordinate  */

/* number-molecules, density, Temperature, time-step, CutOff, Nose's S and V */
double NumMol;
double Rho;
double KbT;
double Tau;
double CutOff;
double UniversalTime;
double S;
double V;

/* number-cycles, recording-frequency */
int NumIter;
int RecFrq;

/* programming variables  */
double CutOff2;
double L;
double r2;
double r2i;
double r6i;
double tmp;
double ff;
double VV2;
int nr;
int nn;
int i;
int j;
int Nread;
char DirName[256] = "~/RedHatBackup/MD-Simulation-ReDo/CanonicalSimulation";
char ParamFileName[256] = "ThreeDMD.Parameters";
char * CurDir;
FILE *fpPar, *fpProp, *fopen();

main(argc, argv)
int argc;
char *argv[];
{
if(chdir(DirName) != 0) exit(99);
if((CurDir = getcwd(NULL,256)) == NULL) exit(1);
printf("CURRENT WORKING DIRECTORY: %s\n\n",CurDir);
/* read input configuration file */
fpPar = fopen("Pippo","r+");
 printf("TRIED OPENING FILE !!! \n");
if(fpPar == NULL)
{
 printf("Can't open Parameter File %s \n\n",ParamFileName);
 perror("fopen failure");
 exit(2);
}
fscanf(fpPar,"%lf ",&NumMol);
fscanf(fpPar,"%lf",&Rho);
fscanf(fpPar,"%lf",&KbT);
fscanf(fpPar,"%lf",&CutOff);
fscanf(fpPar,"%lf",&UniversalTime);
fscanf(fpPar,"%d",&NumIter);
fscanf(fpPar,"%lf",&Tau);
fscanf(fpPar,"%d",&RecFrq);

if((X = (double *)calloc((int)NumMol,sizeof(double)))==NULL) exit(3);
if((Y = (double *)calloc((int)NumMol,sizeof(double)))==NULL) exit(3);
if((Z = (double *)calloc((int)NumMol,sizeof(double)))==NULL) exit(3);
if((Vx = (double *)calloc((int)NumMol,sizeof(double)))==NULL) exit(3);
if((Vy = (double *)calloc((int)NumMol,sizeof(double)))==NULL) exit(3);
if((Vz = (double *)calloc((int)NumMol,sizeof(double)))==NULL) exit(3);
if((Fx = (double *)calloc((int)NumMol,sizeof(double)))==NULL) exit(3);
if((Fy = (double *)calloc((int)NumMol,sizeof(double)))==NULL) exit(3);
if((Fz = (double *)calloc((int)NumMol,sizeof(double)))==NULL) exit(3);
nr=0;
while((Nread=fscanf(fpPar,"%lf %lf %lf %lf %lf %lf",&X[nr],&Y[nr],&Z[nr],&Vx[nr],&Vy[nr],&Vz[nr]))!=EOF) nr++;
if(nr != (int)NumMol) exit(4);

L= cbrt(NumMol/Rho); 
CutOff2= CutOff*CutOff;
S=1;
V=0;
/*###########################################################################################*/
/***          update positions, S parameter, forces, velocities, V parameter               ***/        
/*---------------------------------------  Main Loop START ----------------------------------*/
for(nn=0; nn<NumIter; nn++)
{
 UniversalTime += Tau;
 for(i=0; i<(int)NumMol; i++)
 {
  X[i]+= Tau*Vx[i];
  Y[i]+= Tau*Vy[i];
  Z[i]+= Tau*Vz[i];
 }
 S   += Tau*V;
 for(i=0; i<(int)NumMol; i++)
 {
  Fx[i]=0;
  Fy[i]=0;
  Fz[i]=0;
 }
 for(i=0; i<(int)NumMol-1; i++)
  for(j=i+1; j<(int)NumMol; j++)
  {
   tmp= (X[i]-X[j]) ? (X[i]-X[j]) - L*(int)((X[i]-X[j])/L) + 0.5 : (X[i]-X[j]) - L*(int)((X[i]-X[j])/L) - 0.5; 
   r2=  tmp*tmp;
   tmp= (Y[i]-Y[j]) ? (Y[i]-Y[j]) - L*(int)((Y[i]-Y[j])/L) + 0.5 : (Y[i]-Y[j]) - L*(int)((Y[i]-Y[j])/L) - 0.5;
   r2+= tmp*tmp;
   tmp= (Z[i]-Z[j]) ? (Z[i]-Z[j]) - L*(int)((Z[i]-Z[j])/L) + 0.5 : (Z[i]-Z[j]) - L*(int)((Z[i]-Z[j])/L) - 0.5; 
   r2+= tmp*tmp;
   if(r2>=CutOff2) continue;
   r2i=1.0/r2;
   r6i=r2i*r2i*r2i;
   ff=48*r2i*r6i*(r6i-0.5);
   Fx[i]+=ff*(X[i]-X[j]);
   Fy[i]+=ff*(Y[i]-Y[j]);
   Fz[i]+=ff*(Z[i]-Z[j]);
   Fx[j]-=ff*(X[i]-X[j]);
   Fx[j]-=ff*(X[i]-X[j]);
   Fx[j]-=ff*(X[i]-X[j]);
  }
 VV2=0;
 for(i=0; i<(int)NumMol; i++)
 {
  Vx[i]= Vx[i]*(1- V*Tau/S)*(1- V*Tau/S) + Fx[i]*Tau/(S*S);  
  Vy[i]= Vy[i]*(1- V*Tau/S)*(1- V*Tau/S) + Fy[i]*Tau/(S*S);  
  Vz[i]= Vz[i]*(1- V*Tau/S)*(1- V*Tau/S) + Fz[i]*Tau/(S*S);  
  VV2+= Vx[i]*Vx[i] + Vy[i]*Vy[i] + Vz[i]*Vz[i];
 }
 V+= Tau*(S*VV2 - (3*NumMol +1)*KbT/S); 
}
/*---------------------------------------  Main Loop END ------------------------------------*/
/*###########################################################################################*/

/* write output configuration file */
rewind(fpPar);
fprintf(fpPar,"%lf \n",NumMol);
fprintf(fpPar,"%lf \n",Rho);
fprintf(fpPar,"%lf \n",KbT);
fprintf(fpPar,"%lf \n",CutOff);
fprintf(fpPar,"%lf \n",UniversalTime);
fprintf(fpPar,"%d \n",NumIter);
fprintf(fpPar,"%lf \n",Tau);
fprintf(fpPar,"%d \n",RecFrq);
for(i=0; i<(int)NumMol; i++)
 fprintf(fpPar,"%lf  %lf  %lf  %lf  %lf  %lf \n",X[i],Y[i],Z[i],Vx[i],Vy[i],Vz[i]);
fclose(fpPar);

} 

 
    


--------------F619EEC86E7557089097B822
Content-Type: text/plain; charset=us-ascii;
 name="log"
Content-Transfer-Encoding: 7bit
Content-Disposition: inline;
 filename="log"

[1] <- "(gdb) "
% netscape /usr/share/doc/packages/gvd/gvd.html

--------------F619EEC86E7557089097B822--
Previous message: [gvd-devel] Advertise with E-Mail Marketing!
Next message: [gvd-devel] GVD dies upon opening source file
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]