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fix saed/vtk does not use the overwrite option anywhere

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This commit is contained in:
Axel Kohlmeyer
2021-10-04 17:22:58 -04:00
parent 485796f387
commit dd2b5b22d4
3 changed files with 49 additions and 65 deletions
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5
doc/src/fix_saed_vtk.rst
View File

@ -28,7 +28,6 @@ Syntax
Nstart = start averaging on this timestep
*file* arg = filename
filename = name of file to output time averages to
*overwrite* arg = none = overwrite output file with only latest output
Examples
""""""""
@ -161,10 +160,6 @@ the *file* keyword and this string is appended with _N.vtk where N is
an index (0,1,2...) to account for situations with multiple diffraction
intensity outputs.
The *overwrite* keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of
output. This option can only be used with the *ave running* setting.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

107
src/DIFFRACTION/fix_saed_vtk.cpp
View File

@ -31,6 +31,7 @@
#include <cstring>
#include <cmath>
using namespace LAMMPS_NS;
using namespace FixConst;
@ -100,8 +101,6 @@ FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal fix saed/vtk command");
if (nfreq % nevery || nrepeat*nevery > nfreq)
error->all(FLERR,"Illegal fix saed/vtk command");
if (ave != RUNNING && overwrite)
error->all(FLERR,"Illegal fix saed/vtk command");
// allocate memory for averaging
@ -315,7 +314,7 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep)
if (irepeat == 0)
for (int i = 0; i < nrows; i++)
vector[i] = 0.0;
vector[i] = 0.0;
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
@ -369,7 +368,7 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep)
for (int i = 0; i < nrows; i++) {
vector_total[i] += vector[i];
if (window_limit) vector_total[i] -= vector_list[iwindow][i];
vector_list[iwindow][i] = vector[i];
vector_list[iwindow][i] = vector[i];
}
iwindow++;
@ -391,8 +390,7 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep)
fp = fopen(nName.c_str(),"w");
if (fp == nullptr)
error->one(FLERR,"Cannot open fix saed/vtk file {}: {}",
nName,utils::getsyserror());
error->one(FLERR,"Cannot open fix saed/vtk file {}: {}", nName,utils::getsyserror());
}
fprintf(fp,"# vtk DataFile Version 3.0 c_%s\n",ids);
@ -406,71 +404,68 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep)
fprintf(fp,"SCALARS intensity float\n");
fprintf(fp,"LOOKUP_TABLE default\n");
filepos = ftell(fp);
if (overwrite) fseek(fp,filepos,SEEK_SET);
// Finding the intersection of the reciprical space and Ewald sphere
int NROW1 = 0;
int NROW2 = 0;
double dinv2 = 0.0;
double r = 0.0;
double K[3];
// Finding the intersection of the reciprical space and Ewald sphere
int NROW1 = 0;
int NROW2 = 0;
double dinv2 = 0.0;
double r = 0.0;
double K[3];
// Zone flag to capture entire recrocal space volume
if ((Zone[0] == 0) && (Zone[1] == 0) && (Zone[2] == 0)) {
for (int k = Knmin[2]; k <= Knmax[2]; k++) {
for (int j = Knmin[1]; j <= Knmax[1]; j++) {
for (int i = Knmin[0]; i <= Knmax[0]; i++) {
K[0] = i * dK[0];
K[1] = j * dK[1];
K[2] = k * dK[2];
dinv2 = (K[0] * K[0] + K[1] * K[1] + K[2] * K[2]);
if (dinv2 < Kmax * Kmax) {
fprintf(fp,"%g\n",vector_total[NROW1]/norm);
fflush(fp);
NROW1++;
NROW2++;
} else {
// Zone flag to capture entire recrocal space volume
if ((Zone[0] == 0) && (Zone[1] == 0) && (Zone[2] == 0)) {
for (int k = Knmin[2]; k <= Knmax[2]; k++) {
for (int j = Knmin[1]; j <= Knmax[1]; j++) {
for (int i = Knmin[0]; i <= Knmax[0]; i++) {
K[0] = i * dK[0];
K[1] = j * dK[1];
K[2] = k * dK[2];
dinv2 = (K[0] * K[0] + K[1] * K[1] + K[2] * K[2]);
if (dinv2 < Kmax * Kmax) {
fprintf(fp,"%g\n",vector_total[NROW1]/norm);
fflush(fp);
NROW1++;
NROW2++;
} else {
fprintf(fp,"%d\n",-1);
fflush(fp);
NROW2++;
}
}
}
}
} else {
for (int k = Knmin[2]; k <= Knmax[2]; k++) {
for (int j = Knmin[1]; j <= Knmax[1]; j++) {
for (int i = Knmin[0]; i <= Knmax[0]; i++) {
K[0] = i * dK[0];
K[1] = j * dK[1];
K[2] = k * dK[2];
dinv2 = (K[0] * K[0] + K[1] * K[1] + K[2] * K[2]);
if (dinv2 < Kmax * Kmax) {
r=0.0;
for (int m=0; m<3; m++) r += pow(K[m] - Zone[m],2.0);
r = sqrt(r);
if ( (r > (R_Ewald - dR_Ewald) ) && (r < (R_Ewald + dR_Ewald) )) {
fprintf(fp,"%g\n",vector_total[NROW1]/norm);
fflush(fp);
NROW2++;
NROW1++;
} else {
fprintf(fp,"%d\n",-1);
fflush(fp);
NROW2++;
}
}
} else {
for (int k = Knmin[2]; k <= Knmax[2]; k++) {
for (int j = Knmin[1]; j <= Knmax[1]; j++) {
for (int i = Knmin[0]; i <= Knmax[0]; i++) {
K[0] = i * dK[0];
K[1] = j * dK[1];
K[2] = k * dK[2];
dinv2 = (K[0] * K[0] + K[1] * K[1] + K[2] * K[2]);
if (dinv2 < Kmax * Kmax) {
r=0.0;
for (int m=0; m<3; m++) r += pow(K[m] - Zone[m],2.0);
r = sqrt(r);
if ( (r > (R_Ewald - dR_Ewald) ) && (r < (R_Ewald + dR_Ewald) )) {
fprintf(fp,"%g\n",vector_total[NROW1]/norm);
fflush(fp);
NROW2++;
NROW1++;
} else {
fprintf(fp,"%d\n",-1);
fflush(fp);
NROW2++;
}
} else {
fprintf(fp,"%d\n",-1);
fflush(fp);
NROW2++;
}
}
}
}
}
}
}
nOutput++;
}
@ -497,7 +492,6 @@ void FixSAEDVTK::options(int narg, char **arg)
fp = nullptr;
ave = ONE;
startstep = 0;
overwrite = 0;
// optional args
int iarg = 7;
@ -534,9 +528,6 @@ void FixSAEDVTK::options(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal fix saed/vtk command");
startstep = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"overwrite") == 0) {
overwrite = 1;
iarg += 1;
} else error->all(FLERR,"Illegal fix saed/vtk command");
}
}

2
src/DIFFRACTION/fix_saed_vtk.h
View File

@ -43,8 +43,6 @@ class FixSAEDVTK : public Fix {
int nrows;
int ave, nwindow, nsum, startstep;
int overwrite;
long filepos;
int norm, iwindow, window_limit;
double *vector;