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fix_saed_vtk.cpp
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Sat, Jun 1, 16:56

fix_saed_vtk.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Pieter in 't Veld (SNL)
Incorporating SAED: Shawn Coleman (Arkansas)
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <string.h>
#include "fix_saed_vtk.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "compute_saed.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
#include "force.h"
#include <math.h>
#include "domain.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{COMPUTE};
enum{ONE,RUNNING,WINDOW};
enum{FIRST,MULTI};
#define INVOKED_VECTOR 2
/* ---------------------------------------------------------------------- */
FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), ids(NULL), fp(NULL), vector(NULL),
vector_total(NULL), vector_list(NULL), compute_saed(NULL), filename(NULL)
{
if (narg < 7) error->all(FLERR,"Illegal fix saed/vtk command");
MPI_Comm_rank(world,&me);
nevery = force->inumeric(FLERR,arg[3]);
nrepeat = force->inumeric(FLERR,arg[4]);
nfreq = force->inumeric(FLERR,arg[5]);
global_freq = nfreq;
nvalues = 0;
int iarg = 6;
while (iarg < narg) {
if (strncmp(arg[iarg],"c_",2) == 0){
nvalues++;
iarg++;
} else break;
}
if (nvalues != 1) error->all(FLERR,"Illegal fix saed/vtk command");
options(narg,arg);
which = 0;
ids = NULL;
nvalues = 0;
iarg = 6;
while (iarg < narg) {
if (strncmp(arg[iarg],"c_",2) == 0 ) {
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) error->all(FLERR,"Illegal fix saed/vtk command");
n = strlen(suffix) + 1;
ids = new char[n];
strcpy(ids,suffix);
delete [] suffix;
int icompute = modify->find_compute(ids);
if (icompute < 0)
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 saed/vtk has invalid compute assigned");
// Gather varialbes from specified compute_saed
double *saed_var = compute_saed->saed_var;
lambda = saed_var[0];
Kmax = saed_var[1];
Zone[0] = saed_var[2];
Zone[1] = saed_var[3];
Zone[2] = saed_var[4];
c[0] = saed_var[5];
c[1] = saed_var[6];
c[2] = saed_var[7];
dR_Ewald = saed_var[8];
double manual_double = saed_var[9];
manual = false;
if (manual_double == 1) manual = true;
// Standard error check for fix/ave/time
if (compute->vector_flag == 0)
error->all(FLERR,"Fix saed/vtk compute does not calculate a vector");
if (compute->extvector != 0)
error->all(FLERR,"Illegal fix saed/vtk command");
nrows = compute->size_vector;
nvalues++;
iarg++;
} else break;
}
// setup and error check
// for fix inputs, check that fix frequency is acceptable
if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
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
vector = vector_total = NULL;
vector_list = NULL;
if (ave == WINDOW)
memory->create(vector_list,nwindow,nvalues,"saed/vtk:vector_list");
memory->create(vector,nrows,"saed/vtk:vector");
memory->create(vector_total,nrows,"saed/vtk:vector_total");
extlist = NULL;
vector_flag = 1;
size_vector = nrows;
if (nOutput == 0) {
// SAED specific paramaters needed
int *periodicity = domain->periodicity;
// Zone flag to capture entire recrocal space volume
if ( (Zone[0] == 0) && (Zone[1] == 0) && (Zone[2] == 0) ){
} else {
R_Ewald = (1 / lambda);
double Rnorm = R_Ewald/ sqrt(Zone[0] * Zone[0] +
Zone[1] * Zone[1] + Zone[2]* Zone[2]);
Zone[0] = Zone[0] * Rnorm;
Zone[1] = Zone[1] * Rnorm;
Zone[2] = Zone[2] * Rnorm;
}
double *prd;
double ave_inv = 0.0;
prd = domain->prd;
if (periodicity[0]){
prd_inv[0] = 1 / prd[0];
ave_inv += prd_inv[0];
}
if (periodicity[1]){
prd_inv[1] = 1 / prd[1];
ave_inv += prd_inv[1];
}
if (periodicity[2]){
prd_inv[2] = 1 / prd[2];
ave_inv += prd_inv[2];
}
// Using the average inverse dimensions for non-periodic direction
ave_inv = ave_inv / (periodicity[0] + periodicity[1] + periodicity[2]);
if (!periodicity[0]){
prd_inv[0] = ave_inv;
}
if (!periodicity[1]){
prd_inv[1] = ave_inv;
}
if (!periodicity[2]){
prd_inv[2] = ave_inv;
}
// Use manual mapping of reciprocal lattice
if (manual) {
for (int i=0; i<3; i++) {
prd_inv[i] = 1.0;
}
}
// Find integer dimensions of the reciprocal lattice box bounds
if ( (Zone[0] == 0) && (Zone[1] == 0) && (Zone[2] == 0) ){
for (int i=0; i<3; i++) {
dK[i] = prd_inv[i]*c[i];
Knmax[i] = ceil(Kmax / dK[i]);
Knmin[i] = -Knmax[i];
}
} else {
for (int i=0; i<3; i++) {
Knmax[i] = -10000;
Knmin[i] = 10000;
}
double dinv2 = 0.0;
double r = 0.0;
double K[3];
int Ksearch[3];
for (int i=0; i<3; i++) {
dK[i] = prd_inv[i]*c[i];
Ksearch[i] = ceil(Kmax / dK[i]);
}
for (int k = -Ksearch[2]; k <= Ksearch[2]; k++) {
for (int j = -Ksearch[1]; j <= Ksearch[1]; j++) {
for (int i = -Ksearch[0]; i <= Ksearch[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) ) ){
if ( i < Knmin[0] ) Knmin[0] = i;
if ( j < Knmin[1] ) Knmin[1] = j;
if ( k < Knmin[2] ) Knmin[2] = k;
if ( i > Knmax[0] ) Knmax[0] = i;
if ( j > Knmax[1] ) Knmax[1] = j;
if ( k > Knmax[2] ) Knmax[2] = k;
}
}
}
}
}
}
// Finding dimensions for vtk files
for (int i=0; i<3; i++) {
if ( ( (Knmin[i] > 0) && (Knmax[i] > 0) ) || ( (Knmin[i] < 0) && (Knmax[i] < 0) ) ){
Dim[i] = abs( (int) Knmin[i] ) + abs( (int) Knmax[i] );
} else Dim[i] = abs( (int) Knmin[i] ) + abs( (int) Knmax[i] ) + 1;
}
}
// initialization
irepeat = 0;
iwindow = window_limit = 0;
norm = 0;
for (int i = 0; i < nrows; i++)
vector_total[i] = 0.0;
// nvalid = next step on which end_of_step does something
// add nvalid to all computes that store invocation times
// since don't know a priori which are invoked by this fix
// once in end_of_step() can set timestep for ones actually invoked
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
/* ---------------------------------------------------------------------- */
FixSAEDVTK::~FixSAEDVTK()
{
delete [] extlist;
memory->destroy(vector);
memory->destroy(vector_total);
if (fp && me == 0) fclose(fp);
}
/* ---------------------------------------------------------------------- */
int FixSAEDVTK::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixSAEDVTK::init()
{
// set current indices for all computes,fixes,variables
int icompute = modify->find_compute(ids);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix saed/vtk does not exist");
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
if (nvalid < update->ntimestep) {
irepeat = 0;
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
}
/* ----------------------------------------------------------------------
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
void FixSAEDVTK::setup(int vflag)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixSAEDVTK::end_of_step()
{
// skip if not step which requires doing something
bigint ntimestep = update->ntimestep;
if (ntimestep != nvalid) return;
invoke_vector(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 saed/vtk does not exist");
if (irepeat == 0)
for (int i = 0; i < nrows; i++)
vector[i] = 0.0;
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
// invoke compute if not previously invoked
Compute *compute = modify->compute[icompute];
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
double *vector = compute->vector;
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep+nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// average the final result for the Nfreq timestep
double repeat = nrepeat;
for ( int i = 0; i < nrows; i++)
vector[i] /= repeat;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ave == ONE) {
for (int i = 0; i < nrows; i++) vector_total[i] = vector[i];
norm = 1;
} else if (ave == RUNNING) {
for (int i = 0; i < nrows; i++) vector_total[i] += vector[i];
norm++;
} else if (ave == WINDOW) {
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];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
if (window_limit) norm = nwindow;
else norm = iwindow;
}
// output result to file
if (fp && me == 0) {
if (nOutput > 0) {
fclose(fp);
char nName [128];
sprintf(nName,"%s.%d.vtk",filename,nOutput);
fp = fopen(nName,"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix saed/vtk file %s",nName);
error->one(FLERR,str);
}
}
fprintf(fp,"# vtk DataFile Version 3.0 c_%s\n",ids);
fprintf(fp,"Image data set\n");
fprintf(fp,"ASCII\n");
fprintf(fp,"DATASET STRUCTURED_POINTS\n");
fprintf(fp,"DIMENSIONS %d %d %d\n", Dim[0], Dim[1], Dim[2]);
fprintf(fp,"ASPECT_RATIO %g %g %g\n", dK[0], dK[1], dK[2]);
fprintf(fp,"ORIGIN %g %g %g\n", Knmin[0] * dK[0], Knmin[1] * dK[1], Knmin[2] * dK[2]);
fprintf(fp,"POINT_DATA %d\n", Dim[0] * Dim[1] * Dim[2] );
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];
// 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 {
fprintf(fp,"%d\n",-1);
fflush(fp);
NROW2++;
}
}
}
}
}
}
nOutput++;
}
/* ----------------------------------------------------------------------
return Ith vector value
------------------------------------------------------------------------- */
double FixSAEDVTK::compute_vector(int i)
{
if (norm) {
return vector_total[i]/norm;
}
return 0.0;
}
/* ----------------------------------------------------------------------
parse optional args
------------------------------------------------------------------------- */
void FixSAEDVTK::options(int narg, char **arg)
{
// option defaults
fp = NULL;
ave = ONE;
startstep = 0;
overwrite = 0;
// optional args
int iarg = 6 + nvalues;
while (iarg < narg) {
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix saed/vtk command");
if (me == 0) {
nOutput = 0;
int n = strlen(arg[iarg+1]) + 1;
filename = new char[n];
strcpy(filename,arg[iarg+1]);
char nName [128];
sprintf(nName,"%s.%d.vtk",filename,nOutput);
fp = fopen(nName,"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix saed/vtk file %s",nName);
error->one(FLERR,str);
}
}
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix saed/vtk command");
if (strcmp(arg[iarg+1],"one") == 0) ave = ONE;
else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING;
else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW;
else error->all(FLERR,"Illegal fix saed/vtk command");
if (ave == WINDOW) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix saed/vtk command");
nwindow = force->inumeric(FLERR,arg[iarg+2]);
if (nwindow <= 0) error->all(FLERR,"Illegal fix saed/vtk command");
}
iarg += 2;
if (ave == WINDOW) iarg++;
} else if (strcmp(arg[iarg],"start") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix saed/vtk command");
startstep = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"overwrite") == 0) {
overwrite = 1;
iarg += 1;
} else error->all(FLERR,"Illegal fix saed/vtk command");
}
}
/* ----------------------------------------------------------------------
calculate nvalid = next step on which end_of_step does something
can be this timestep if multiple of nfreq and nrepeat = 1
else backup from next multiple of nfreq
startstep is lower bound on nfreq multiple
------------------------------------------------------------------------- */
bigint FixSAEDVTK::nextvalid()
{
bigint nvalid = (update->ntimestep/nfreq)*nfreq + nfreq;
while (nvalid < startstep) nvalid += nfreq;
if (nvalid-nfreq == update->ntimestep && nrepeat == 1)
nvalid = update->ntimestep;
else
nvalid -= (nrepeat-1)*nevery;
if (nvalid < update->ntimestep) nvalid += nfreq;
return nvalid;
}
/* ---------------------------------------------------------------------- */
void FixSAEDVTK::reset_timestep(bigint ntimestep)
{
if (ntimestep > nvalid) error->all(FLERR,"Fix saed/vtk missed timestep");
}

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