git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1059 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -22,18 +22,21 @@
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#include "modify.h"
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#include "compute.h"
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#include "group.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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enum{COMPUTE,FIX};
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enum{SCALAR,VECTOR,BOTH};
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enum{ONE,RUNNING,WINDOW};
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/* ---------------------------------------------------------------------- */
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FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg != 10) error->all("Illegal fix ave/time command");
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if (narg < 8) error->all("Illegal fix ave/time command");
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MPI_Comm_rank(world,&me);
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@ -49,16 +52,53 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
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id = new char[n];
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strcpy(id,arg[7]);
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int flag = atoi(arg[8]);
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// option defaults
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if (strcmp(arg[9],"NULL") == 0) fp = NULL;
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else if (me == 0) {
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fp = fopen(arg[9],"w");
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if (fp == NULL) {
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char str[128];
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sprintf(str,"Cannot open fix ave/time file %s",arg[9]);
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error->one(str);
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}
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sflag = 1;
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vflag = 0;
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fp = NULL;
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ave = ONE;
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// optional args
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int iarg = 8;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"type") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix ave/time command");
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if (strcmp(arg[iarg+1],"scalar") == 0) {
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sflag = 1;
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vflag = 0;
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} else if (strcmp(arg[iarg+1],"vector") == 0) {
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sflag = 0;
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vflag = 1;
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} else if (strcmp(arg[iarg+1],"both") == 0) sflag = vflag = 1;
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else error->all("Illegal fix ave/time command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"file") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix ave/time command");
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if (me == 0) {
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fp = fopen(arg[iarg+1],"w");
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if (fp == NULL) {
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char str[128];
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sprintf(str,"Cannot open fix ave/time file %s",arg[iarg+1]);
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error->one(str);
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}
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}
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iarg += 2;
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} else if (strcmp(arg[iarg],"ave") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix ave/time command");
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if (strcmp(arg[iarg+1],"one") == 0) ave = ONE;
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else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING;
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else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW;
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else error->all("Illegal fix ave/time command");
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if (ave == WINDOW) {
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if (iarg+3 > narg) error->all("Illegal fix ave/time command");
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nwindow = atoi(arg[iarg+2]);
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if (nwindow <= 0) error->all("Illegal fix ave/time command");
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}
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iarg += 2;
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if (ave == WINDOW) iarg++;
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} else error->all("Illegal fix ave/time command");
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}
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// setup and error check
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@ -76,11 +116,6 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
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if (ifix < 0) error->all("Fix ID for fix ave/time does not exist");
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}
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if (flag < 0 || flag > 2) error->all("Illegal fix ave/time command");
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sflag = vflag = 0;
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if (flag == 0 || flag == 2) sflag = 1;
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if (flag == 1 || flag == 2) vflag = 1;
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if (which == COMPUTE) {
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if (sflag && modify->compute[icompute]->scalar_flag == 0)
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error->all("Fix ave/time compute does not calculate a scalar");
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@ -121,15 +156,25 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
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fprintf(fp,"TimeStep Scalar-value Vector-values\n");
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}
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vector = NULL;
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// allocate memory for averaging
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vector = vector_total = NULL;
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if (vflag) {
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if (which == COMPUTE) size_vector = modify->compute[icompute]->size_vector;
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else size_vector = modify->fix[ifix]->size_vector;
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vector = new double[size_vector];
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vector_total = new double[size_vector];
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for (int i = 0; i < size_vector; i++) vector_total[i] = 0.0;
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}
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scalar_list = NULL;
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vector_list = NULL;
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if (sflag && ave == WINDOW) scalar_list = new double[nwindow];
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if (vflag && ave == WINDOW)
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vector_list = memory->create_2d_double_array(nwindow,size_vector,
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"fix ave/time:vector_list");
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// enable this fix to produce a global scalar and/or vector
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// initialize values to 0.0 since thermo may call them on first step
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if (sflag) scalar_flag = 1;
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if (vflag) vector_flag = 1;
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@ -137,15 +182,23 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
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if (which == COMPUTE) extensive = modify->compute[icompute]->extensive;
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else extensive = modify->fix[ifix]->extensive;
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scalar = 0.0;
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for (int i = 0; i < size_vector; i++) vector[i] = 0.0;
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// nvalid = next step on which end_of_step does something
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// initializations
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irepeat = 0;
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iwindow = window_limit = 0;
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norm = 0;
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// nvalid = next step on which end_of_step does something
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// can be this timestep if multiple of nfreq and nrepeat = 1
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// else backup from next multiple of nfreq
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nvalid = (update->ntimestep/nfreq)*nfreq + nfreq;
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nvalid -= (nrepeat-1)*nevery;
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if (nvalid <= update->ntimestep)
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if (nvalid-nfreq == update->ntimestep && nrepeat == 1)
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nvalid = update->ntimestep;
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else
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nvalid -= (nrepeat-1)*nevery;
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if (nvalid < update->ntimestep)
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error->all("Fix ave/time cannot be started on this timestep");
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}
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@ -157,6 +210,9 @@ FixAveTime::~FixAveTime()
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if (fp && me == 0) fclose(fp);
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delete [] compute;
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delete [] vector;
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delete [] vector_total;
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delete [] scalar_list;
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memory->destroy_2d_double_array(vector_list);
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}
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/* ---------------------------------------------------------------------- */
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@ -204,6 +260,15 @@ void FixAveTime::init()
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}
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}
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/* ----------------------------------------------------------------------
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only does something if nvalid = current timestep
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------------------------------------------------------------------------- */
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void FixAveTime::setup()
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{
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end_of_step();
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}
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/* ---------------------------------------------------------------------- */
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void FixAveTime::end_of_step()
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@ -243,45 +308,89 @@ void FixAveTime::end_of_step()
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vector[i] += fix->compute_vector(i);
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}
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// done if irepeat < nrepeat
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irepeat++;
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nvalid += nevery;
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if (irepeat < nrepeat) return;
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// output the results
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// average the final result for the Nfreq timestep
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// reset irepeat and nvalid
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if (irepeat == nrepeat) {
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double repeat = nrepeat;
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if (sflag) scalar /= repeat;
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if (vflag) for (i = 0; i < size_vector; i++) vector[i] /= repeat;
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double repeat = nrepeat;
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if (sflag) scalar /= repeat;
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if (vflag) for (i = 0; i < size_vector; i++) vector[i] /= repeat;
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if (fp && me == 0) {
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fprintf(fp,"%d",update->ntimestep);
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if (sflag) fprintf(fp," %g",scalar);
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if (vflag)
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for (i = 0; i < size_vector; i++) fprintf(fp," %g",vector[i]);
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fprintf(fp,"\n");
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fflush(fp);
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irepeat = 0;
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nvalid = update->ntimestep+nfreq - (nrepeat-1)*nevery;
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// if ave = ONE, only single Nfreq timestep value is needed
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// if ave = RUNNING, combine with all previous Nfreq timestep values
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// if ave = WINDOW, comine with nwindow most recent Nfreq timestep values
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if (ave == ONE) {
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if (sflag) scalar_total = scalar;
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if (vflag) for (i = 0; i < size_vector; i++) vector_total[i] = vector[i];
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norm = 1;
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} else if (ave == RUNNING) {
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if (sflag) scalar_total += scalar;
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if (vflag) for (i = 0; i < size_vector; i++) vector_total[i] += vector[i];
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norm++;
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} else if (ave == WINDOW) {
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if (sflag) {
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scalar_total += scalar;
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if (window_limit) scalar_total -= scalar_list[iwindow];
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scalar_list[iwindow] = scalar;
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}
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if (vflag) {
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for (i = 0; i < size_vector; i++) {
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vector_total[i] += vector[i];
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if (window_limit) vector_total[i] -= vector_list[iwindow][i];
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vector_list[iwindow][i] = vector[i];
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}
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}
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irepeat = 0;
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nvalid = update->ntimestep+nfreq - (nrepeat-1)*nevery;
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iwindow++;
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if (iwindow == nwindow) {
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iwindow = 0;
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window_limit = 1;
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}
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if (window_limit) norm = nwindow;
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else norm = iwindow;
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}
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// output result to file
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if (fp && me == 0) {
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fprintf(fp,"%d",update->ntimestep);
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if (sflag) fprintf(fp," %g",scalar_total/norm);
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if (vflag)
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for (i = 0; i < size_vector; i++) fprintf(fp," %g",vector_total[i]/norm);
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fprintf(fp,"\n");
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fflush(fp);
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}
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}
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/* ----------------------------------------------------------------------
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return scalar value
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could be ONE, RUNNING, or WINDOW value
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------------------------------------------------------------------------- */
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double FixAveTime::compute_scalar()
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{
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return scalar;
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if (norm) return scalar_total/norm;
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return 0.0;
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}
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/* ----------------------------------------------------------------------
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return Nth vector value
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could be ONE, RUNNING, or WINDOW value
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------------------------------------------------------------------------- */
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double FixAveTime::compute_vector(int n)
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{
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return vector[n];
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if (norm) return vector_total[n]/norm;
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else return 0.0;
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}
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