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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3512 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2009-12-09 21:12:49 +00:00
parent 41f61f38c7
commit 8b6877e6d0
21 changed files with 885 additions and 363 deletions
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86
src/fix_ave_spatial.cpp
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@ -36,7 +36,8 @@ enum{X,V,F,DENSITY_NUMBER,DENSITY_MASS,COMPUTE,FIX,VARIABLE};
enum{SAMPLE,ALL};
enum{BOX,LATTICE,REDUCED};
enum{ONE,RUNNING,WINDOW};
enum{DUMMY0,INVOKED_SCALAR,INVOKED_VECTOR,DUMMMY3,INVOKED_PERATOM};
#define INVOKED_PERATOM 8
#define BIG 1000000000
@ -154,6 +155,9 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
scaleflag = LATTICE;
fp = NULL;
ave = ONE;
char *title1 = NULL;
char *title2 = NULL;
char *title3 = NULL;
while (iarg < narg) {
if (strcmp(arg[iarg],"norm") == 0) {
@ -193,6 +197,27 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
}
iarg += 2;
if (ave == WINDOW) iarg++;
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
delete [] title1;
int n = strlen(arg[iarg+1]) + 1;
title1 = new char[n];
strcpy(title1,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title2") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
delete [] title2;
int n = strlen(arg[iarg+1]) + 1;
title2 = new char[n];
strcpy(title2,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title3") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
delete [] title3;
int n = strlen(arg[iarg+1]) + 1;
title3 = new char[n];
strcpy(title3,arg[iarg+1]);
iarg += 2;
} else error->all("Illegal fix ave/spatial command");
}
@ -243,27 +268,38 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
}
}
// print header into file
// print file comment lines
if (fp && me == 0) {
fprintf(fp,"# Spatial-averaged data for fix %s and group %s\n",id,arg[1]);
fprintf(fp,"# TimeStep Number-of-layers\n");
fprintf(fp,"# Layer Coordinate Natoms");
for (int i = 0; i < nvalues; i++)
if (which[i] == COMPUTE) fprintf(fp," c_%s",ids[i]);
else if (which[i] == FIX) fprintf(fp," f_%s",ids[i]);
else if (which[i] == VARIABLE) fprintf(fp," v_%s",ids[i]);
else fprintf(fp," %s",arg[9+i]);
fprintf(fp,"\n");
if (title1) fprintf(fp,"%s\n",title1);
else fprintf(fp,"# Spatial-averaged data for fix %s and group %s\n",
id,arg[1]);
if (title2) fprintf(fp,"%s\n",title2);
else fprintf(fp,"# Timestep Number-of-layers\n");
if (title3) fprintf(fp,"%s\n",title3);
else {
fprintf(fp,"# Layer Coord Ncount");
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) fprintf(fp," c_%s",ids[i]);
else if (which[i] == FIX) fprintf(fp," f_%s",ids[i]);
else if (which[i] == VARIABLE) fprintf(fp," v_%s",ids[i]);
else fprintf(fp," %s",arg[9+i]);
}
fprintf(fp,"\n");
}
}
// this fix produces a global vector
// set size_vector to BIG since compute_vector() checks bounds on-the-fly
vector_flag = 1;
size_vector = BIG;
delete [] title1;
delete [] title2;
delete [] title3;
// this fix produces a global array
array_flag = 1;
size_local_rows = BIG;
size_local_cols = nvalues+2;
global_freq = nfreq;
extvector = 0;
extarray = 0;
// setup scaling
@ -803,18 +839,18 @@ void FixAveSpatial::end_of_step()
}
/* ----------------------------------------------------------------------
return Nth vector value
since values_sum is 2d array, map N into ilayer and ivalue
if ilayer exceeds current layers, return 0.0 instead of generate an error
return I,J array value
if I exceeds current layers, return 0.0 instead of generating an error
1st column = bin coord, 2nd column = count, remaining columns = Nvalues
------------------------------------------------------------------------- */
double FixAveSpatial::compute_vector(int n)
double FixAveSpatial::compute_array(int i, int j)
{
int ivalue = n % nvalues;
int ilayer = n / nvalues;
if (ilayer >= nlayers) return 0.0;
if (values_total == NULL) return 0.0;
return values_total[ilayer][ivalue]/norm;
if (i >= nlayers) return 0.0;
if (j == 0) return coord[i];
if (j == 1) return count_total[i]/norm;
return values_total[i][j]/norm;
}
/* ----------------------------------------------------------------------