ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3533 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2009-12-15 16:19:15 +00:00
parent 4a18836003
commit 18f7ebff4f
2 changed files with 180 additions and 56 deletions
Download Patch File Download Diff File Expand all files Collapse all files

226
src/fix_ave_histo.cpp
View File

@ -126,6 +126,7 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
}
// setup and error check
// kind = inputs are all global, or all per-atom, or all local
// for fix inputs, check that fix frequency is acceptable
if (nevery <= 0) error->all("Illegal fix ave/histo command");
@ -135,98 +136,172 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
if (lo >= hi) error->all("Illegal fix ave/histo command");
if (nbins <= 0) error->all("Illegal fix ave/histo command");
int kindflag;
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE && mode == SCALAR) {
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[modify->find_compute(ids[0])];
if (compute->scalar_flag || compute->vector_flag || compute->array_flag)
kindflag = GLOBAL;
else if (compute->peratom_flag) kindflag = PERATOM;
else if (compute->local_flag) kindflag = LOCAL;
else error->all("Fix ave/histo input is invalid compute");
} else if (which[i] == FIX) {
Fix *fix = modify->fix[modify->find_fix(ids[0])];
if (fix->scalar_flag || fix->vector_flag || fix->array_flag)
kindflag = GLOBAL;
else if (fix->peratom_flag) kindflag = PERATOM;
else if (fix->local_flag) kindflag = LOCAL;
else error->all("Fix ave/histo input is invalid fix");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (input->variable->equalstyle(ivariable)) kindflag = GLOBAL;
else if (input->variable->atomstyle(ivariable)) kindflag = PERATOM;
else error->all("Fix ave/histo input is invalid variable");
}
if (i == 0) kind = kindflag;
else if (kindflag != kind)
error->all("Fix ave/histo inputs are not all global, peraton, or local");
}
if (kind == PERATOM && mode == SCALAR)
error->all("Fix ave/histo cannot input per-atom values in scalar mode");
if (kind == LOCAL && mode == SCALAR)
error->all("Fix ave/histo cannot input local values in scalar mode");
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE && kind == GLOBAL && mode == SCALAR) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/histo does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0)
error->all("Fix ave/histo compute does not calculate a scalar");
error->all("Fix ave/histo compute does not calculate a global scalar");
if (argindex[i] && modify->compute[icompute]->vector_flag == 0)
error->all("Fix ave/histo compute does not calculate a vector");
error->all("Fix ave/histo compute does not calculate a global vector");
if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector)
error->all("Fix ave/histo compute vector is accessed out-of-range");
} else if (which[i] == COMPUTE && mode == VECTOR) {
} else if (which[i] == COMPUTE && kind == GLOBAL && mode == VECTOR) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/histo does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->vector_flag == 0)
error->all("Fix ave/histo compute does not calculate a vector");
error->all("Fix ave/histo compute does not calculate a global vector");
if (argindex[i] && modify->compute[icompute]->array_flag == 0)
error->all("Fix ave/histo compute does not calculate a array");
error->all("Fix ave/histo compute does not calculate a global array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_array_cols)
error->all("Fix ave/histo compute array is accessed out-of-range");
} else if (which[i] == FIX && mode == SCALAR) {
} else if (which[i] == COMPUTE && kind == PERATOM) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/histo does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Fix ave/histo compute does not calculate per-atom values");
if (argindex[i] == 0 &&
modify->compute[icompute]->size_peratom_cols != 0)
error->all("Fix ave/histo compute does not "
"calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
error->all("Fix ave/histo compute does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_peratom_cols)
error->all("Fix ave/histo compute array is accessed out-of-range");
} else if (which[i] == COMPUTE && kind == LOCAL) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/histo does not exist");
if (modify->compute[icompute]->local_flag == 0)
error->all("Fix ave/histo compute does not calculate local values");
if (argindex[i] == 0 &&
modify->compute[icompute]->size_local_cols != 0)
error->all("Fix ave/histo compute does not "
"calculate a local vector");
if (argindex[i] && modify->compute[icompute]->size_local_cols == 0)
error->all("Fix ave/histo compute does not "
"calculate a local array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_local_cols)
error->all("Fix ave/histo compute array is accessed out-of-range");
} else if (which[i] == FIX && kind == GLOBAL && mode == SCALAR) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/histo does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
error->all("Fix ave/histo fix does not calculate a scalar");
error->all("Fix ave/histo fix does not calculate a global scalar");
if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
error->all("Fix ave/histo fix does not calculate a vector");
error->all("Fix ave/histo fix does not calculate a global vector");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector)
error->all("Fix ave/histo fix vector is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
error->all("Fix for fix ave/histo not computed at compatible time");
} else if (which[i] == FIX && mode == VECTOR) {
} else if (which[i] == FIX && kind == GLOBAL && mode == VECTOR) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/histo does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
error->all("Fix ave/histo fix does not calculate a vector");
if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
error->all("Fix ave/histo fix does not calculate a array");
if (argindex[i] == 0 && modify->fix[ifix]->vector_flag == 0)
error->all("Fix ave/histo fix does not calculate a global vector");
if (argindex[i] && modify->fix[ifix]->array_flag == 0)
error->all("Fix ave/histo fix does not calculate a global array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_array_cols)
error->all("Fix ave/histo fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
error->all("Fix for fix ave/histo not computed at compatible time");
} else if (which[i] == VARIABLE && mode == SCALAR) {
} else if (which[i] == FIX && kind == PERATOM) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/histo does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
error->all("Fix ave/histo fix does not calculate per-atom values");
if (argindex[i] == 0 &&
modify->fix[ifix]->size_peratom_cols != 0)
error->all("Fix ave/histo fix does not "
"calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
error->all("Fix ave/histo fix does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->fix[ifix]->size_peratom_cols)
error->all("Fix ave/histo fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
error->all("Fix for fix ave/histo not computed at compatible time");
} else if (which[i] == FIX && kind == LOCAL) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/histo does not exist");
if (modify->fix[ifix]->local_flag == 0)
error->all("Fix ave/histo fix does not calculate local values");
if (argindex[i] == 0 &&
modify->fix[ifix]->size_local_cols != 0)
error->all("Fix ave/histo fix does not "
"calculate a local vector");
if (argindex[i] && modify->fix[ifix]->size_local_cols == 0)
error->all("Fix ave/histo fix does not "
"calculate a local array");
if (argindex[i] &&
argindex[i] > modify->fix[ifix]->size_local_cols)
error->all("Fix ave/histo fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
error->all("Fix for fix ave/histo not computed at compatible time");
} else if (which[i] == VARIABLE && kind == GLOBAL) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for fix ave/histo does not exist");
if (input->variable->equalstyle(ivariable) == 0)
error->all("Fix ave/histo variable is not equal-style variable");
} else if (which[i] == VARIABLE && mode == VECTOR) {
} else if (which[i] == VARIABLE && kind == PERATOM) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for fix ave/histo does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all("Fix ave/histo variable is not atom-style variable");
}
}
// check that inputs are all global, or all per-atom, or all local
int kindflag;
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[modify->find_compute(ids[0])];
if (compute->scalar_flag || compute->vector_flag || compute->scalar_flag)
kindflag = GLOBAL;
else if (compute->peratom_flag) kindflag = PERATOM;
else kindflag = LOCAL;
} else if (which[i] == FIX) {
Fix *fix = modify->fix[modify->find_fix(ids[0])];
if (fix->scalar_flag || fix->vector_flag || fix->scalar_flag)
kindflag = GLOBAL;
else if (fix->peratom_flag) kindflag = PERATOM;
else kindflag = LOCAL;
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (input->variable->equalstyle(ivariable) == 0) kindflag = GLOBAL;
else kindflag = PERATOM;
}
if (i == 0) kind = kindflag;
else if (kindflag != kind)
error->all("Fix ave/histo inputs are not all global, peraton, or local");
}
// print file comment lines
if (fp && me == 0) {
@ -252,12 +327,20 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
bin_total = new double[nbins];
bin_all = new double[nbins];
coord = new double[nbins];
vector = NULL;
maxatom = 0;
// initializations
// set coord to bin centers
double binsize = hi - lo;
bininv = binsize/nbins;
if (beyond == EXTRA) {
binsize = (hi-lo)/(nbins-2);
bininv = 1.0/binsize;
} else {
binsize = (hi-lo)/nbins;
bininv = 1.0/binsize;
}
if (beyond == EXTRA) {
coord[0] = lo;
coord[nbins-1] = hi;
@ -308,6 +391,7 @@ FixAveHisto::~FixAveHisto()
delete [] bin_total;
delete [] bin_all;
delete [] coord;
memory->sfree(vector);
}
/* ---------------------------------------------------------------------- */
@ -427,7 +511,8 @@ void FixAveHisto::end_of_step()
if (argindex[i] == 0)
bin_atoms(compute->vector_atom,1);
else
bin_atoms(compute->array_atom[argindex[i]-1],size_peratom_cols);
bin_atoms(compute->array_atom[argindex[i]-1],
compute->size_peratom_cols);
} else if (kind == LOCAL) {
if (!(compute->invoked_flag & INVOKED_LOCAL)) {
@ -446,10 +531,48 @@ void FixAveHisto::end_of_step()
} else if (which[i] == FIX) {
Fix *fix = modify->fix[m];
if (kind == GLOBAL && mode == SCALAR) {
if (argindex[i] == 0) bin_one(fix->compute_scalar());
else bin_one(fix->compute_vector(argindex[i]-1));
} else if (kind == GLOBAL && mode == VECTOR) {
if (argindex[i] == 0) {
int n = fix->size_vector;
for (i = 0; i < n; i++) bin_one(fix->compute_vector(i));
} else {
int j = argindex[i] - 1;
int n = fix->size_vector;
for (i = 0; i < n; i++) bin_one(fix->compute_array(i,j));
}
} else if (kind == PERATOM) {
if (argindex[i] == 0) bin_atoms(fix->vector_atom,1);
else bin_atoms(fix->array_atom[argindex[i]-1],fix->size_peratom_cols);
} else if (kind == LOCAL) {
if (argindex[i] == 0)
bin_vector(fix->size_local_rows,fix->vector_local,1);
else
bin_vector(fix->size_local_rows,fix->array_local[argindex[i]-1],
fix->size_local_cols);
}
// evaluate equal-style variable
} else if (which[i] == VARIABLE) {
//scalar = input->variable->compute_equal(m);
} else if (which[i] == VARIABLE && kind == GLOBAL) {
bin_one(input->variable->compute_equal(m));
} else if (which[i] == VARIABLE && kind == PERATOM) {
if (atom->nlocal > maxatom) {
memory->sfree(vector);
maxatom = atom->nmax;
vector = (double *) memory->smalloc(maxatom*sizeof(double),
"fix_ave/histo:vector");
}
input->variable->compute_atom(m,igroup,vector,1,0);
bin_atoms(vector,1);
}
}
@ -581,7 +704,6 @@ void FixAveHisto::bin_one(double value)
}
stats[0] += 1.0;
stats[0] += 1.0;
}
/* ----------------------------------------------------------------------

10
src/fix_ave_histo.h
View File

@ -36,16 +36,18 @@ class FixAveHisto : public Fix {
int *which,*argindex,*value2index;
char **ids;
FILE *fp;
double lo,hi;
double bininv;
double lo,hi,binsize,bininv;
int kind,beyond;
double stats[4],stats_total[4],stats_all[4];
int nbins;
double *bin,*bin_total,*bin_all;
double *coord;
double **bin_list;
double *coord;
double stats[4],stats_total[4],stats_all[4];
double *vector;
int maxatom;
int ave,nwindow,nsum,startstep,mode;
char *title1,*title2,*title3;