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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13668 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2015-07-21 23:48:07 +00:00
parent 9aee122766
commit 1ddb1601f3
3 changed files with 76 additions and 72 deletions
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54
src/USER-DIFFRACTION/fix_saed_vtk.cpp
View File

@ -18,7 +18,7 @@
#include "stdlib.h"
#include "string.h"
#include "fix_ave_time_saed.h"
#include "fix_saed_vtk.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
@ -47,10 +47,10 @@ enum{FIRST,MULTI};
/* ---------------------------------------------------------------------- */
FixAveTimeSAED::FixAveTimeSAED(LAMMPS *lmp, int narg, char **arg) :
FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 7) error->all(FLERR,"Illegal fix ave/time/saed command");
if (narg < 7) error->all(FLERR,"Illegal fix saed/vtk command");
MPI_Comm_rank(world,&me);
@ -68,7 +68,7 @@ FixAveTimeSAED::FixAveTimeSAED(LAMMPS *lmp, int narg, char **arg) :
iarg++;
} else break;
}
if (nvalues != 1) error->all(FLERR,"Illegal fix ave/time/saed command");
if (nvalues != 1) error->all(FLERR,"Illegal fix saed/vtk command");
options(narg,arg);
@ -87,7 +87,7 @@ FixAveTimeSAED::FixAveTimeSAED(LAMMPS *lmp, int narg, char **arg) :
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) error->all(FLERR,"Illegal fix ave/time/saed command");
if (ptr) error->all(FLERR,"Illegal fix saed/vtk command");
n = strlen(suffix) + 1;
ids = new char[n];
@ -96,14 +96,14 @@ FixAveTimeSAED::FixAveTimeSAED(LAMMPS *lmp, int narg, char **arg) :
int icompute = modify->find_compute(ids);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix ave/time/saed does not exist");
error->all(FLERR,"Compute ID for fix saed/vtk does not exist");
Compute *compute = modify->compute[icompute];
// Check that specified compute is for SAED
compute_saed = (ComputeSAED*) modify->compute[icompute];
if (strcmp(compute_saed->style,"saed") != 0)
error->all(FLERR,"Fix ave/time/saed has invalid compute assigned");
error->all(FLERR,"Fix saed/vtk has invalid compute assigned");
// Gather varialbes from specified compute_saed
double *saed_var = compute_saed->saed_var;
@ -122,9 +122,9 @@ FixAveTimeSAED::FixAveTimeSAED(LAMMPS *lmp, int narg, char **arg) :
// Standard error check for fix/ave/time
if (compute->vector_flag == 0)
error->all(FLERR,"Fix ave/time/saed compute does not calculate a vector");
error->all(FLERR,"Fix saed/vtk compute does not calculate a vector");
if (compute->extvector != 0)
error->all(FLERR,"Illegal fix ave/time/saed command");
error->all(FLERR,"Illegal fix saed/vtk command");
int length = modify->compute[icompute]->size_vector;
@ -138,11 +138,11 @@ FixAveTimeSAED::FixAveTimeSAED(LAMMPS *lmp, int narg, char **arg) :
// for fix inputs, check that fix frequency is acceptable
if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
error->all(FLERR,"Illegal fix ave/time/saed command");
error->all(FLERR,"Illegal fix saed/vtk command");
if (nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
error->all(FLERR,"Illegal fix ave/time/saed command");
error->all(FLERR,"Illegal fix saed/vtk command");
if (ave != RUNNING && overwrite)
error->all(FLERR,"Illegal fix ave/time/saed command");
error->all(FLERR,"Illegal fix saed/vtk command");
// allocate memory for averaging
@ -150,10 +150,10 @@ FixAveTimeSAED::FixAveTimeSAED(LAMMPS *lmp, int narg, char **arg) :
vector_list = NULL;
if (ave == WINDOW)
memory->create(vector_list,nwindow,nvalues,"ave/time/saed:vector_list");
memory->create(vector_list,nwindow,nvalues,"saed/vtk:vector_list");
memory->create(vector,nrows,"ave/time/saed:vector");
memory->create(vector_total,nrows,"ave/time/saed:vector_total");
memory->create(vector,nrows,"saed/vtk:vector");
memory->create(vector_total,nrows,"saed/vtk:vector_total");
extlist = NULL;
@ -290,7 +290,7 @@ FixAveTimeSAED::FixAveTimeSAED(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
FixAveTimeSAED::~FixAveTimeSAED()
FixSAEDVTK::~FixSAEDVTK()
{
delete [] extlist;
memory->destroy(vector);
@ -300,7 +300,7 @@ FixAveTimeSAED::~FixAveTimeSAED()
/* ---------------------------------------------------------------------- */
int FixAveTimeSAED::setmask()
int FixSAEDVTK::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
@ -309,7 +309,7 @@ int FixAveTimeSAED::setmask()
/* ---------------------------------------------------------------------- */
void FixAveTimeSAED::init()
void FixSAEDVTK::init()
{
// set current indices for all computes,fixes,variables
@ -331,14 +331,14 @@ void FixAveTimeSAED::init()
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
void FixAveTimeSAED::setup(int vflag)
void FixSAEDVTK::setup(int vflag)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixAveTimeSAED::end_of_step()
void FixSAEDVTK::end_of_step()
{
// skip if not step which requires doing something
bigint ntimestep = update->ntimestep;
@ -348,12 +348,12 @@ void FixAveTimeSAED::end_of_step()
/* ---------------------------------------------------------------------- */
void FixAveTimeSAED::invoke_vector(bigint ntimestep)
void FixSAEDVTK::invoke_vector(bigint ntimestep)
{
// zero if first step
int icompute = modify->find_compute(ids);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix ave/time/saed does not exist");
error->all(FLERR,"Compute ID for fix saed/vtk does not exist");
if (irepeat == 0)
for (int i = 0; i < nrows; i++)
@ -435,7 +435,7 @@ void FixAveTimeSAED::invoke_vector(bigint ntimestep)
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix ave/time/saed file %s",nName);
sprintf(str,"Cannot open fix saed/vtk file %s",nName);
error->one(FLERR,str);
}
}
@ -523,7 +523,7 @@ void FixAveTimeSAED::invoke_vector(bigint ntimestep)
return Ith vector value
------------------------------------------------------------------------- */
double FixAveTimeSAED::compute_vector(int i)
double FixSAEDVTK::compute_vector(int i)
{
if (norm) {
return vector_total[i]/norm;
@ -535,7 +535,7 @@ double FixAveTimeSAED::compute_vector(int i)
parse optional args
------------------------------------------------------------------------- */
void FixAveTimeSAED::options(int narg, char **arg)
void FixSAEDVTK::options(int narg, char **arg)
{
// option defaults
@ -598,7 +598,7 @@ void FixAveTimeSAED::options(int narg, char **arg)
startstep is lower bound on nfreq multiple
------------------------------------------------------------------------- */
bigint FixAveTimeSAED::nextvalid()
bigint FixSAEDVTK::nextvalid()
{
bigint nvalid = (update->ntimestep/nfreq)*nfreq + nfreq;
while (nvalid < startstep) nvalid += nfreq;
@ -612,7 +612,7 @@ bigint FixAveTimeSAED::nextvalid()
/* ---------------------------------------------------------------------- */
void FixAveTimeSAED::reset_timestep(bigint ntimestep)
void FixSAEDVTK::reset_timestep(bigint ntimestep)
{
if (ntimestep > nvalid) error->all(FLERR,"Fix saed/vtk missed timestep");
}

12
src/USER-DIFFRACTION/fix_saed_vtk.h
View File

@ -13,22 +13,22 @@
#ifdef FIX_CLASS
FixStyle(ave/time/saed,FixAveTimeSAED)
FixStyle(saed/vtk,FixSAEDVTK)
#else
#ifndef LMP_FIX_AVE_TIME_SAED_H
#define LMP_FIX_AVE_TIME_SAED_H
#ifndef LMP_FIX_SAED_VTK_H
#define LMP_FIX_SAED_VTK_H
#include "stdio.h"
#include "fix.h"
namespace LAMMPS_NS {
class FixAveTimeSAED : public Fix {
class FixSAEDVTK : public Fix {
public:
FixAveTimeSAED(class LAMMPS *, int, char **);
~FixAveTimeSAED();
FixSAEDVTK(class LAMMPS *, int, char **);
~FixSAEDVTK();
int setmask();
void init();
void setup(int);

82
src/fix_ave_histo.cpp
View File

@ -26,9 +26,6 @@
#include "error.h"
#include "force.h"
#include <iostream>
using namespace std;
using namespace LAMMPS_NS;
using namespace FixConst;
@ -46,6 +43,7 @@ enum{SINGLE,VALUE};
#define INVOKED_LOCAL 16
#define BIG 1.0e20
/* ---------------------------------------------------------------------- */
FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
@ -193,7 +191,8 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
if (mode == VECTOR && which[nvalues] == COMPUTE &&
argindex[nvalues] == 0) {
if (weights = VALUE) error->all(FLERR,"Illegal fix ave/histo command");
if (weights == VALUE)
error->all(FLERR,"Illegal fix ave/histo command");
int icompute = modify->find_compute(ids[nvalues]);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix ave/histo does not exist");
@ -214,7 +213,8 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
} else if (mode == VECTOR && which[nvalues] == FIX &&
argindex[nvalues] == 0) {
if (weights = VALUE) error->all(FLERR,"Illegal fix ave/histo command");
if (weights == VALUE)
error->all(FLERR,"Illegal fix ave/histo command");
int ifix = modify->find_fix(ids[nvalues]);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix ave/histo does not exist");
@ -439,41 +439,45 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
}
// weighted histogram number of rows must match weights
int Size[2];
if ( weights == VALUE ) {
int size[2];
if (weights == VALUE) {
// NOTE: shouldn't this be one?
if (nvalues != 2) error->all(FLERR,"Illegal fix ave/histo command");
for (int i = 0; i < nvalues; i++) {
if (which[i] == X || which[i] == V || which[i] == F) {
Size[i] = atom->nmax;
} else if (which[i] == COMPUTE && kind == GLOBAL && mode == SCALAR) {
int icompute = modify->find_compute(ids[i]);
Size[i] = modify->compute[icompute]->size_vector;
} else if (which[i] == COMPUTE && kind == GLOBAL && mode == VECTOR) {
int icompute = modify->find_compute(ids[i]);
Size[i] = modify->compute[icompute]->size_array_rows;
} else if (which[i] == COMPUTE && kind == PERATOM) {
int icompute = modify->find_compute(ids[i]);
Size[i] = atom->nmax;
} else if (which[i] == COMPUTE && kind == LOCAL) {
int icompute = modify->find_compute(ids[i]);
Size[i] = modify->compute[icompute]->size_local_rows;
} else if (which[i] == FIX && kind == GLOBAL && mode == SCALAR) {
int ifix = modify->find_fix(ids[i]);
Size[i] = modify->fix[ifix]->size_vector;
} else if (which[i] == FIX && kind == GLOBAL && mode == VECTOR) {
int ifix = modify->find_fix(ids[i]);
Size[i]= modify->fix[ifix]->size_array_rows;
} else if (which[i] == FIX && kind == PERATOM) {
int ifix = modify->find_fix(ids[i]);
Size[i] = atom->nmax;
} else if (which[i] == FIX && kind == LOCAL) {
int ifix = modify->find_fix(ids[i]);
Size[i] = modify->fix[ifix]->size_local_rows;
} else if (which[i] == VARIABLE && kind == PERATOM) {
Size[i] = atom->nmax;
}
}
if (Size[0] != Size[1]) error->all(FLERR,"Illegal fix ave/histo command");
if (which[i] == X || which[i] == V || which[i] == F) {
size[i] = atom->nmax;
} else if (which[i] == COMPUTE && kind == GLOBAL && mode == SCALAR) {
int icompute = modify->find_compute(ids[i]);
size[i] = modify->compute[icompute]->size_vector;
} else if (which[i] == COMPUTE && kind == GLOBAL && mode == VECTOR) {
int icompute = modify->find_compute(ids[i]);
size[i] = modify->compute[icompute]->size_array_rows;
} else if (which[i] == COMPUTE && kind == PERATOM) {
int icompute = modify->find_compute(ids[i]);
size[i] = atom->nmax;
} else if (which[i] == COMPUTE && kind == LOCAL) {
int icompute = modify->find_compute(ids[i]);
size[i] = modify->compute[icompute]->size_local_rows;
} else if (which[i] == FIX && kind == GLOBAL && mode == SCALAR) {
int ifix = modify->find_fix(ids[i]);
size[i] = modify->fix[ifix]->size_vector;
} else if (which[i] == FIX && kind == GLOBAL && mode == VECTOR) {
int ifix = modify->find_fix(ids[i]);
size[i]= modify->fix[ifix]->size_array_rows;
} else if (which[i] == FIX && kind == PERATOM) {
int ifix = modify->find_fix(ids[i]);
size[i] = atom->nmax;
} else if (which[i] == FIX && kind == LOCAL) {
int ifix = modify->find_fix(ids[i]);
size[i] = modify->fix[ifix]->size_local_rows;
} else if (which[i] == VARIABLE && kind == PERATOM) {
size[i] = atom->nmax;
}
}
if (size[0] != size[1])
error->all(FLERR,"Fix ave/histo value and weight vector "
"lengths do not match");
}
// print file comment lines
@ -1395,7 +1399,7 @@ void FixAveHisto::options(int narg, char **arg)
(strncmp(arg[iarg],"f_",2) == 0) ||
(strncmp(arg[iarg],"v_",2) == 0)) {
iarg++;
}
} error->all(FLERR,"Illegal fix ave/histo command");
nvalues = 2;
weights = VALUE;
} else error->all(FLERR,"Illegal fix ave/histo command");