git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1272 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -22,21 +22,25 @@
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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 "input.h"
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#include "variable.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{COMPUTE,FIX,VARIABLE};
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enum{ONE,RUNNING,WINDOW};
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#define INVOKED_SCALAR 1 // same as in computes
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#define INVOKED_VECTOR 2
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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 < 8) error->all("Illegal fix ave/time command");
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if (narg < 7) error->all("Illegal fix ave/time command");
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MPI_Comm_rank(world,&me);
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@ -44,37 +48,55 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
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nrepeat = atoi(arg[4]);
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nfreq = atoi(arg[5]);
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if (strcmp(arg[6],"compute") == 0) which = COMPUTE;
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else if (strcmp(arg[6],"fix") == 0) which = FIX;
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else error->all("Illegal fix ave/time command");
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// parse values until one isn't recognized
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int n = strlen(arg[7]) + 1;
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id = new char[n];
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strcpy(id,arg[7]);
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which = new int[narg-6];
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argindex = new int[narg-6];
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ids = new char*[narg-6];
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value2index = new int[narg-6];
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nvalues = 0;
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int iarg = 6;
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while (iarg < narg) {
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if ((strncmp(arg[iarg],"c_",2) == 0) ||
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(strncmp(arg[iarg],"f_",2) == 0) ||
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(strncmp(arg[iarg],"v_",2) == 0)) {
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if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
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else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
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else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
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int n = strlen(arg[iarg]);
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char *suffix = new char[n];
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strcpy(suffix,&arg[iarg][2]);
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char *ptr = strchr(suffix,'[');
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if (ptr) {
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if (suffix[strlen(suffix)-1] != ']')
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error->all("Illegal fix ave/time command");
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argindex[nvalues] = atoi(ptr+1);
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*ptr = '\0';
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} else argindex[nvalues] = 0;
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n = strlen(suffix) + 1;
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ids[nvalues] = new char[n];
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strcpy(ids[nvalues],suffix);
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nvalues++;
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delete [] suffix;
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} else break;
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iarg++;
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}
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// option defaults
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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 (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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@ -107,85 +129,108 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
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if (nfreq < nevery || nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
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error->all("Illegal fix ave/time command");
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int icompute,ifix;
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if (which == COMPUTE) {
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icompute = modify->find_compute(id);
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if (icompute < 0) error->all("Compute ID for fix ave/time does not exist");
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} else {
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ifix = modify->find_fix(id);
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if (ifix < 0) error->all("Fix ID for fix ave/time does not exist");
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for (int i = 0; i < nvalues; i++) {
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if (which[i] == COMPUTE) {
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int icompute = modify->find_compute(ids[i]);
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if (icompute < 0)
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error->all("Compute ID for fix ave/time does not exist");
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if (argindex[i] == 0 && 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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if (argindex[i] && modify->compute[icompute]->vector_flag == 0)
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error->all("Fix ave/time compute does not calculate a vector");
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if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector)
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error->all("Fix ave/time compute vector is accessed out-of-range");
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} else if (which[i] == FIX) {
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int ifix = modify->find_fix(ids[i]);
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if (ifix < 0)
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error->all("Fix ID for fix ave/time does not exist");
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if (argindex[i] && modify->fix[ifix]->scalar_flag == 0)
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error->all("Fix ave/time fix does not calculate a scalar");
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if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
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error->all("Fix ave/time fix does not calculate a vector");
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if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector)
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error->all("Fix ave/time fix vector is accessed out-of-range");
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} else if (which[i] == VARIABLE) {
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int ivariable = input->variable->find(ids[i]);
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if (ivariable < 0)
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error->all("Variable name for fix ave/time does not exist");
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if (input->variable->equalstyle(ivariable) == 0)
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error->all("Fix ave/time variable is not equal-style variable");
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}
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}
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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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if (vflag && modify->compute[icompute]->vector_flag == 0)
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error->all("Fix ave/time compute does not calculate a vector");
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} else {
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if (sflag && modify->fix[ifix]->scalar_flag == 0)
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error->all("Fix ave/time fix does not calculate a scalar");
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if (vflag && modify->fix[ifix]->vector_flag == 0)
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error->all("Fix ave/time fix does not calculate a vector");
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}
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// setup list of computes to call, including pre-computes
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compute = NULL;
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if (which == COMPUTE) {
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ncompute = 1 + modify->compute[icompute]->npre;
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compute = new Compute*[ncompute];
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} else ncompute = 0;
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// print header into file
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if (fp && me == 0) {
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if (which == COMPUTE)
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fprintf(fp,"Time-averaged data for fix %s, group %s, and compute %s\n",
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id,group->names[modify->compute[icompute]->igroup],id);
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else
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fprintf(fp,"Time-averaged data for fix %s, group %s, and fix %s\n",
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id,group->names[modify->fix[ifix]->igroup],id);
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if (sflag and !vflag)
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fprintf(fp,"TimeStep Value\n");
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else if (!sflag and vflag)
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fprintf(fp,"TimeStep Vector-values\n");
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else if (!sflag and vflag)
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fprintf(fp,"TimeStep Scalar-value Vector-values\n");
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fprintf(fp,"Time-averaged data for fix %s\n",id);
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fprintf(fp,"TimeStep");
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for (int i = 0; i < nvalues; i++)
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if (which[i] == COMPUTE) fprintf(fp," c_%s",ids[i]);
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else if (which[i] == FIX) fprintf(fp," f_%s",ids[i]);
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else if (which[i] == VARIABLE) fprintf(fp," v_%s",ids[i]);
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fprintf(fp,"\n");
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}
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// allocate memory for averaging
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// allocate and initialize 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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}
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vector = new double[nvalues];
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vector_total = new double[nvalues];
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for (int i = 0; i < nvalues; i++) vector_total[i] = 0.0;
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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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if (ave == WINDOW)
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vector_list = memory->create_2d_double_array(nwindow,nvalues,
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"ave/time:vector_list");
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// enable this fix to produce a global scalar and/or vector
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// this fix produces either a global scalar or vector
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// intensive/extensive flags set by compute,fix,variable that produces value
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if (sflag) scalar_flag = 1;
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if (vflag) vector_flag = 1;
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scalar_vector_freq = nfreq;
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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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extlist = NULL;
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if (nvalues == 1) {
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scalar_flag = 1;
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if (which[0] == COMPUTE) {
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Compute *compute = modify->compute[modify->find_compute(ids[0])];
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if (argindex[0] == 0) extscalar = compute->extscalar;
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else if (compute->extvector >= 0) extscalar = compute->extvector;
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else extscalar = compute->extlist[argindex[0]-1];
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} else if (which[0] == FIX) {
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Fix *fix = modify->fix[modify->find_fix(ids[0])];
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if (argindex[0] == 0) extscalar = fix->extscalar;
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else if (fix->extvector >= 0) extscalar = fix->extvector;
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else extscalar = fix->extlist[argindex[0]-1];
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} else if (which[0] == VARIABLE)
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extscalar = 0;
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} else {
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vector_flag = 1;
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size_vector = nvalues;
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extvector = -1;
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extlist = new int[nvalues];
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for (int i = 0; i < nvalues; i++) {
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if (which[i] == COMPUTE) {
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Compute *compute = modify->compute[modify->find_compute(ids[i])];
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if (argindex[i] == 0) extlist[i] = compute->extscalar;
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else if (compute->extvector >= 0) extlist[i] = compute->extvector;
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else extlist[i] = compute->extlist[argindex[i]-1];
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} else if (which[i] == FIX) {
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Fix *fix = modify->fix[modify->find_fix(ids[i])];
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if (argindex[i] == 0) extlist[i] = fix->extscalar;
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else if (fix->extvector >= 0) extlist[i] = fix->extvector;
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else extlist[i] = fix->extlist[argindex[i]-1];
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} else if (which[i] == VARIABLE)
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extlist[i] = 0;
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}
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}
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// initializations
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// set scalar and vector total to zero since they accumulate
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// set vector total to zero since it accumulates
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irepeat = 0;
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iwindow = window_limit = 0;
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norm = 0;
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scalar_total = 0.0;
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if (vflag) for (int i = 0; i < size_vector; i++) vector_total[i] = 0.0;
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for (int i = 0; i < nvalues; i++) vector_total[i] = 0.0;
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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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@ -198,24 +243,27 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
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nvalid -= (nrepeat-1)*nevery;
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if (nvalid < update->ntimestep) nvalid += nfreq;
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// set timestep for all computes that store invocation times
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// since don't know a priori which are invoked by this fix
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// add nvalid to ALL computes that store invocation times
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// since don't know a priori which are invoked by this fix
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// once in end_of_step() can just set timestep for ones actually invoked
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for (int i = 0; i < modify->ncompute; i++)
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if (modify->compute[i]->timeflag) modify->compute[i]->add_step(nvalid);
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modify->addstep_compute_all(nvalid);
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}
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/* ---------------------------------------------------------------------- */
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FixAveTime::~FixAveTime()
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{
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delete [] id;
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delete [] which;
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delete [] argindex;
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for (int i = 0; i < nvalues; i++) delete [] ids[i];
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delete [] ids;
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delete [] value2index;
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delete [] extlist;
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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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@ -232,36 +280,33 @@ int FixAveTime::setmask()
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void FixAveTime::init()
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{
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// set ptrs to compute and its pre-computes called each end-of-step
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// put pre-computes in list before compute
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if (which == COMPUTE) {
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int icompute = modify->find_compute(id);
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if (icompute < 0)
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error->all("Compute ID for fix ave/time does not exist");
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ncompute = 0;
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if (modify->compute[icompute]->npre)
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for (int i = 0; i < modify->compute[icompute]->npre; i++) {
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int ic = modify->find_compute(modify->compute[icompute]->id_pre[i]);
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if (ic < 0)
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error->all("Precompute ID for fix ave/time does not exist");
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compute[ncompute++] = modify->compute[ic];
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}
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compute[ncompute++] = modify->compute[icompute];
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}
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// set ptr to fix ID
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// set indices and check validity of all computes,fixes,variables
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// check that fix frequency is acceptable
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if (which == FIX) {
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int ifix = modify->find_fix(id);
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if (ifix < 0)
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error->all("Fix ID for fix ave/time does not exist");
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fix = modify->fix[ifix];
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if (nevery % fix->scalar_vector_freq)
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error->all("Fix ave/time and fix not computed at compatible times");
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int ilist = 0;
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for (int i = 0; i < nvalues; i++) {
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if (which[i] == COMPUTE) {
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int icompute = modify->find_compute(ids[i]);
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if (icompute < 0)
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error->all("Compute ID for fix ave/time does not exist");
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value2index[i] = icompute;
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} else if (which[i] == FIX) {
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int ifix = modify->find_fix(ids[i]);
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if (ifix < 0)
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error->all("Fix ID for fix ave/time does not exist");
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value2index[i] = ifix;
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if (nevery % modify->fix[ifix]->scalar_vector_freq)
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error->all("Fix for fix ave/time not computed at compatible time");
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} else if (which[i] == VARIABLE) {
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int ivariable = input->variable->find(ids[i]);
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if (ivariable < 0)
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error->all("Variable name for fix ave/time does not exist");
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value2index[i] = ivariable;
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}
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}
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}
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@ -278,7 +323,8 @@ void FixAveTime::setup()
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void FixAveTime::end_of_step()
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{
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int i;
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int i,j,k,m;
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double tmp;
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// skip if not step which requires doing something
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@ -286,33 +332,44 @@ void FixAveTime::end_of_step()
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// zero if first step
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if (irepeat == 0) {
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scalar = 0.0;
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if (vflag)
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for (i = 0; i < size_vector; i++) vector[i] = 0.0;
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}
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if (irepeat == 0)
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for (i = 0; i < nvalues; i++) vector[i] = 0.0;
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// accumulate results of compute or fix to local copy
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if (which == COMPUTE) {
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modify->clearstep_compute();
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// accumulate results of computes,fixes,variables to local copy
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// compute/fix/variable may invoke computes so wrap with clear/add
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if (sflag) {
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double value;
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for (i = 0; i < ncompute; i++) value = compute[i]->compute_scalar();
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scalar += value;
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}
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if (vflag) {
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for (i = 0; i < ncompute; i++) compute[i]->compute_vector();
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double *cvector = compute[ncompute-1]->vector;
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for (i = 0; i < size_vector; i++) vector[i] += cvector[i];
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}
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modify->clearstep_compute();
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} else {
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if (sflag) scalar += fix->compute_scalar();
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if (vflag)
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for (i = 0; i < size_vector; i++)
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vector[i] += fix->compute_vector(i);
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int ilist = 0;
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for (i = 0; i < nvalues; i++) {
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m = value2index[i];
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// invoke compute if not previously invoked
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if (which[i] == COMPUTE) {
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Compute *compute = modify->compute[m];
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if (argindex[i] == 0) {
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if (compute->invoked & INVOKED_SCALAR) vector[i] += compute->scalar;
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else vector[i] += compute->compute_scalar();
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} else {
|
||||
if (!(compute->invoked & INVOKED_VECTOR)) compute->compute_vector();
|
||||
vector[i] += compute->vector[argindex[i]-1];
|
||||
}
|
||||
|
||||
// access fix fields, guaranteed to be ready
|
||||
|
||||
} else if (which[i] == FIX) {
|
||||
if (argindex[i] == 0)
|
||||
vector[i] += modify->fix[m]->compute_scalar();
|
||||
else
|
||||
vector[i] += modify->fix[m]->compute_vector(argindex[i]-1);
|
||||
|
||||
// evaluate equal-style variable
|
||||
|
||||
} else if (which[i] == VARIABLE)
|
||||
vector[i] += input->variable->compute_equal(m);
|
||||
}
|
||||
|
||||
// done if irepeat < nrepeat
|
||||
@ -321,46 +378,36 @@ void FixAveTime::end_of_step()
|
||||
irepeat++;
|
||||
if (irepeat < nrepeat) {
|
||||
nvalid += nevery;
|
||||
if (which == COMPUTE) modify->addstep_compute(nvalid);
|
||||
modify->addstep_compute(nvalid);
|
||||
return;
|
||||
}
|
||||
|
||||
irepeat = 0;
|
||||
nvalid = update->ntimestep+nfreq - (nrepeat-1)*nevery;
|
||||
if (which == COMPUTE) modify->addstep_compute(nvalid);
|
||||
modify->addstep_compute(nvalid);
|
||||
|
||||
// average the final result for the Nfreq timestep
|
||||
|
||||
double repeat = nrepeat;
|
||||
if (sflag) scalar /= repeat;
|
||||
if (vflag) for (i = 0; i < size_vector; i++) vector[i] /= repeat;
|
||||
for (i = 0; i < nvalues; 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, comine with nwindow most recent Nfreq timestep values
|
||||
|
||||
if (ave == ONE) {
|
||||
if (sflag) scalar_total = scalar;
|
||||
if (vflag) for (i = 0; i < size_vector; i++) vector_total[i] = vector[i];
|
||||
for (i = 0; i < nvalues; i++) vector_total[i] = vector[i];
|
||||
norm = 1;
|
||||
|
||||
} else if (ave == RUNNING) {
|
||||
if (sflag) scalar_total += scalar;
|
||||
if (vflag) for (i = 0; i < size_vector; i++) vector_total[i] += vector[i];
|
||||
for (i = 0; i < nvalues; i++) vector_total[i] += vector[i];
|
||||
norm++;
|
||||
|
||||
} else if (ave == WINDOW) {
|
||||
if (sflag) {
|
||||
scalar_total += scalar;
|
||||
if (window_limit) scalar_total -= scalar_list[iwindow];
|
||||
scalar_list[iwindow] = scalar;
|
||||
}
|
||||
if (vflag) {
|
||||
for (i = 0; i < size_vector; i++) {
|
||||
vector_total[i] += vector[i];
|
||||
if (window_limit) vector_total[i] -= vector_list[iwindow][i];
|
||||
vector_list[iwindow][i] = vector[i];
|
||||
}
|
||||
for (i = 0; i < nvalues; i++) {
|
||||
vector_total[i] += vector[i];
|
||||
if (window_limit) vector_total[i] -= vector_list[iwindow][i];
|
||||
vector_list[iwindow][i] = vector[i];
|
||||
}
|
||||
|
||||
iwindow++;
|
||||
@ -376,9 +423,7 @@ void FixAveTime::end_of_step()
|
||||
|
||||
if (fp && me == 0) {
|
||||
fprintf(fp,"%d",update->ntimestep);
|
||||
if (sflag) fprintf(fp," %g",scalar_total/norm);
|
||||
if (vflag)
|
||||
for (i = 0; i < size_vector; i++) fprintf(fp," %g",vector_total[i]/norm);
|
||||
for (i = 0; i < nvalues; i++) fprintf(fp," %g",vector_total[i]/norm);
|
||||
fprintf(fp,"\n");
|
||||
fflush(fp);
|
||||
}
|
||||
@ -391,7 +436,7 @@ void FixAveTime::end_of_step()
|
||||
|
||||
double FixAveTime::compute_scalar()
|
||||
{
|
||||
if (norm) return scalar_total/norm;
|
||||
if (norm) return vector_total[0]/norm;
|
||||
return 0.0;
|
||||
}
|
||||
|
||||
|
||||
Reference in New Issue
Block a user