git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14134 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
785
src/USER-MISC/fix_ave_correlate_long.cpp
Normal file
785
src/USER-MISC/fix_ave_correlate_long.cpp
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@ -0,0 +1,785 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Scalar Correlator f(tau)=<A(t)A(t+tau)> and
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Cross-correlator f(tau)=<A(t)B(t+tau)>
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Structure and syntax of fix inspired by fix_ave_correlate
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J. Chem. Phys. 133, 154103 (2010)
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Contributing authors:
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Jorge Ramirez (jorge.ramirez@upm.es, Universidad Politecnica de Madrid),
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Alexei Likhtman (University of Reading)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdlib.h"
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#include "string.h"
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#include "unistd.h"
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#include "fix_ave_correlate_long.h"
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#include "update.h"
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#include "modify.h"
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#include "compute.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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#include "force.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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enum{COMPUTE,FIX,VARIABLE};
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enum{AUTO,UPPER,LOWER,AUTOUPPER,AUTOLOWER,FULL};
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#define INVOKED_SCALAR 1
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#define INVOKED_VECTOR 2
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#define INVOKED_ARRAY 4
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/* ---------------------------------------------------------------------- */
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FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
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Fix (lmp, narg, arg)
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{
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// At least nevery nfrez and one value are needed
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if (narg < 6) error->all(FLERR,"Illegal fix ave/correlate/long command");
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MPI_Comm_rank(world,&me);
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nevery = force->inumeric(FLERR,arg[3]);
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nfreq = force->inumeric(FLERR,arg[4]);
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restart_global = 1;
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global_freq = nfreq;
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// parse values until one isn't recognized
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which = new int[narg-5];
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argindex = new int[narg-5];
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ids = new char*[narg-5];
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value2index = new int[narg-5];
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nvalues = 0;
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int iarg = 5;
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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(FLERR,"Illegal fix ave/correlate/long 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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delete [] suffix;
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nvalues++;
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iarg++;
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} else break;
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}
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// optional args
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type = AUTO;
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startstep = 0;
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fp = NULL;
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overwrite = 0;
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numcorrelators=20;
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p = 16;
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m = 2;
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char *title1 = NULL;
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char *title2 = NULL;
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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)
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error->all(FLERR,"Illegal fix ave/correlate/long command");
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if (strcmp(arg[iarg+1],"auto") == 0) type = AUTO;
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else if (strcmp(arg[iarg+1],"upper") == 0) type = UPPER;
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else if (strcmp(arg[iarg+1],"lower") == 0) type = LOWER;
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else if (strcmp(arg[iarg+1],"auto/upper") == 0) type = AUTOUPPER;
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else if (strcmp(arg[iarg+1],"auto/lower") == 0) type = AUTOLOWER;
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else if (strcmp(arg[iarg+1],"full") == 0) type = FULL;
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else error->all(FLERR,"Illegal fix ave/correlate/long command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"start") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal fix ave/correlate/long command");
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startstep = force->inumeric(FLERR,arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"ncorr") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal fix ave/correlate/long command");
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numcorrelators = force->inumeric(FLERR,arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"p") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal fix ave/correlate/long command");
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p = force->inumeric(FLERR,arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"m") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal fix ave/correlate/long command");
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m = force->inumeric(FLERR,arg[iarg+1]);
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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)
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error->all(FLERR,"Illegal fix ave/correlate/long 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/correlate/long file %s",arg[iarg+1]);
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error->one(FLERR,str);
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}
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}
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iarg += 2;
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} else if (strcmp(arg[iarg],"overwrite") == 0) {
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overwrite = 1;
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iarg += 1;
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} else if (strcmp(arg[iarg],"title1") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal fix ave/correlate/long command");
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delete [] title1;
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int n = strlen(arg[iarg+1]) + 1;
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title1 = new char[n];
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strcpy(title1,arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"title2") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal fix ave/correlate/long command");
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delete [] title2;
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int n = strlen(arg[iarg+1]) + 1;
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title2 = new char[n];
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strcpy(title2,arg[iarg+1]);
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iarg += 2;
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} else error->all(FLERR,"Illegal fix ave/correlate/long command");
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}
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if (p % m != 0) error->all(FLERR,"fix_correlator: p mod m must be 0");
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dmin = p/m;
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length = numcorrelators*p;
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npcorr = 0;
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kmax = 0;
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// setup and error check
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// for fix inputs, check that fix frequency is acceptable
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if (nevery <= 0 || nfreq <= 0)
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error->all(FLERR,"Illegal fix ave/correlate/long command");
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if (nfreq % nevery)
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error->all(FLERR,"Illegal fix ave/correlate/long command");
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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(FLERR,"Compute ID for fix ave/correlate/long does not exist");
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if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0)
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error->all(FLERR,
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"Fix ave/correlate/long 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(FLERR,
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"Fix ave/correlate/long 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(FLERR,"Fix ave/correlate/long compute vector "
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"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(FLERR,"Fix ID for fix ave/correlate/long does not exist");
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if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
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error->all(FLERR,"Fix ave/correlate/long 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(FLERR,"Fix ave/correlate/long 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(FLERR,
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"Fix ave/correlate/long fix vector is accessed out-of-range");
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if (nevery % modify->fix[ifix]->global_freq)
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error->all(FLERR,"Fix for fix ave/correlate/long "
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"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(FLERR,"Variable name for fix ave/correlate/long does not exist");
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if (input->variable->equalstyle(ivariable) == 0)
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error->all(FLERR,
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"Fix ave/correlate/long variable is not equal-style variable");
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}
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}
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// npair = # of correlation pairs to calculate
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if (type == AUTO) npair = nvalues;
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if (type == UPPER || type == LOWER) npair = nvalues*(nvalues-1)/2;
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if (type == AUTOUPPER || type == AUTOLOWER) npair = nvalues*(nvalues+1)/2;
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if (type == FULL) npair = nvalues*nvalues;
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// print file comment lines
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if (fp && me == 0) {
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if (title1) fprintf(fp,"%s\n",title1);
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else fprintf(fp,"# Time-correlated data for fix %s\n",id);
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if (title2) fprintf(fp,"%s\n",title2);
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else {
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fprintf(fp,"# Time");
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if (type == AUTO)
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for (int i = 0; i < nvalues; i++)
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fprintf(fp," %s*%s",arg[5+i],arg[5+i]);
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else if (type == UPPER)
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for (int i = 0; i < nvalues; i++)
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for (int j = i+1; j < nvalues; j++)
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fprintf(fp," %s*%s",arg[5+i],arg[5+j]);
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else if (type == LOWER)
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for (int i = 0; i < nvalues; i++)
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for (int j = 0; j < i-1; j++)
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fprintf(fp," %s*%s",arg[5+i],arg[5+j]);
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else if (type == AUTOUPPER)
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for (int i = 0; i < nvalues; i++)
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for (int j = i; j < nvalues; j++)
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fprintf(fp," %s*%s",arg[5+i],arg[5+j]);
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else if (type == AUTOLOWER)
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for (int i = 0; i < nvalues; i++)
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for (int j = 0; j < i; j++)
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fprintf(fp," %s*%s",arg[5+i],arg[5+j]);
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else if (type == FULL)
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for (int i = 0; i < nvalues; i++)
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for (int j = 0; j < nvalues; j++)
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fprintf(fp," %s*%s",arg[5+i],arg[5+j]);
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fprintf(fp,"\n");
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}
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filepos = ftell(fp);
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}
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delete [] title1;
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delete [] title2;
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// allocate and initialize memory for calculated values and correlators
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memory->create(values,nvalues,"correlator:values");
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memory->create(shift,npair,numcorrelators,p,"correlator:shift");
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memory->create(shift2,npair,numcorrelators,p,"correlator:shift2"); //NOT OPTMAL
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memory->create(correlation,npair,numcorrelators,p,"correlator:correlation");
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memory->create(accumulator,npair,numcorrelators,"correlator:accumulator");
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memory->create(accumulator2,npair,numcorrelators,"correlator:accumulator2"); // NOT OPTIMAL
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memory->create(ncorrelation,numcorrelators,p,"correlator:ncorrelation");
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memory->create(naccumulator,numcorrelators,"correlator:naccumulator");
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memory->create(insertindex,numcorrelators,"correlator:insertindex");
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memory->create(t,length,"correlator:t");
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memory->create(f,npair,length,"correlator:f");
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for (int i=0;i<npair;i++)
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for (int j=0;j<numcorrelators;j++) {
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for (int k=0;k<p;k++) {
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shift[i][j][k]=-2E10;
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shift2[i][j][k]=0.0;
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correlation[i][j][k]=0.0;
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}
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accumulator[i][j]=0.0;
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accumulator2[i][j]=0.0;
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}
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for (int i=0;i<numcorrelators;i++) {
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for (int j=0;j<p;j++) ncorrelation[i][j]=0;
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naccumulator[i]=0;
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insertindex[i]=0;
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}
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for (int i=0;i<length;i++) t[i]=0.0;
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for (int i=0;i<npair;i++)
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for (int j=0;j<length;j++) f[i][j]=0.0;
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||||
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||||
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// nvalid = next step on which end_of_step does something
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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 set timestep for ones actually invoked
|
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|
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nvalid_last = -1;
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nvalid = nextvalid();
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modify->addstep_compute_all(nvalid);
|
||||
}
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||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixAveCorrelateLong::~FixAveCorrelateLong()
|
||||
{
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||||
delete [] which;
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||||
delete [] argindex;
|
||||
delete [] value2index;
|
||||
for (int i = 0; i < nvalues; i++) delete [] ids[i];
|
||||
delete [] ids;
|
||||
|
||||
memory->destroy(values);
|
||||
memory->destroy(shift);
|
||||
memory->destroy(shift2);
|
||||
memory->destroy(correlation);
|
||||
memory->destroy(accumulator);
|
||||
memory->destroy(accumulator2);
|
||||
memory->destroy(ncorrelation);
|
||||
memory->destroy(naccumulator);
|
||||
memory->destroy(insertindex);
|
||||
memory->destroy(t);
|
||||
memory->destroy(f);
|
||||
|
||||
if (fp && me == 0) fclose(fp);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixAveCorrelateLong::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= END_OF_STEP;
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixAveCorrelateLong::init()
|
||||
{
|
||||
// set current indices for all computes,fixes,variables
|
||||
|
||||
for (int i = 0; i < nvalues; i++) {
|
||||
if (which[i] == COMPUTE) {
|
||||
int icompute = modify->find_compute(ids[i]);
|
||||
if (icompute < 0)
|
||||
error->all(FLERR,"Compute ID for fix ave/correlate/long does not exist");
|
||||
value2index[i] = icompute;
|
||||
|
||||
} else if (which[i] == FIX) {
|
||||
int ifix = modify->find_fix(ids[i]);
|
||||
if (ifix < 0)
|
||||
error->all(FLERR,"Fix ID for fix ave/correlate/long does not exist");
|
||||
value2index[i] = ifix;
|
||||
|
||||
} else if (which[i] == VARIABLE) {
|
||||
int ivariable = input->variable->find(ids[i]);
|
||||
if (ivariable < 0)
|
||||
error->all(FLERR,"Variable name for fix ave/correlate/long does not exist");
|
||||
value2index[i] = ivariable;
|
||||
}
|
||||
}
|
||||
|
||||
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
|
||||
|
||||
if (nvalid < update->ntimestep) {
|
||||
nvalid = nextvalid();
|
||||
modify->addstep_compute_all(nvalid);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
only does something if nvalid = current timestep
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixAveCorrelateLong::setup(int vflag)
|
||||
{
|
||||
end_of_step();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixAveCorrelateLong::end_of_step()
|
||||
{
|
||||
int i,m;
|
||||
double scalar;
|
||||
|
||||
// skip if not step which requires doing something
|
||||
// error check if timestep was reset in an invalid manner
|
||||
|
||||
bigint ntimestep = update->ntimestep;
|
||||
if (ntimestep < nvalid_last || ntimestep > nvalid)
|
||||
error->all(FLERR,"Invalid timestep reset for fix ave/correlate/long");
|
||||
if (ntimestep != nvalid) return;
|
||||
nvalid_last = nvalid;
|
||||
|
||||
// accumulate results of computes,fixes,variables to origin
|
||||
// compute/fix/variable may invoke computes so wrap with clear/add
|
||||
|
||||
modify->clearstep_compute();
|
||||
|
||||
for (i = 0; i < nvalues; i++) {
|
||||
m = value2index[i];
|
||||
|
||||
// invoke compute if not previously invoked
|
||||
|
||||
if (which[i] == COMPUTE) {
|
||||
Compute *compute = modify->compute[m];
|
||||
|
||||
if (argindex[i] == 0) {
|
||||
if (!(compute->invoked_flag & INVOKED_SCALAR)) {
|
||||
compute->compute_scalar();
|
||||
compute->invoked_flag |= INVOKED_SCALAR;
|
||||
}
|
||||
scalar = compute->scalar;
|
||||
} else {
|
||||
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
|
||||
compute->compute_vector();
|
||||
compute->invoked_flag |= INVOKED_VECTOR;
|
||||
}
|
||||
scalar = compute->vector[argindex[i]-1];
|
||||
}
|
||||
|
||||
// access fix fields, guaranteed to be ready
|
||||
|
||||
} else if (which[i] == FIX) {
|
||||
if (argindex[i] == 0)
|
||||
scalar = modify->fix[m]->compute_scalar();
|
||||
else
|
||||
scalar = modify->fix[m]->compute_vector(argindex[i]-1);
|
||||
|
||||
// evaluate equal-style variable
|
||||
|
||||
} else if (which[i] == VARIABLE)
|
||||
scalar = input->variable->compute_equal(m);
|
||||
|
||||
values[i] = scalar;
|
||||
}
|
||||
|
||||
// fistindex = index in values ring of earliest time sample
|
||||
|
||||
nvalid += nevery;
|
||||
modify->addstep_compute(nvalid);
|
||||
|
||||
// calculate all Cij() enabled by latest values
|
||||
|
||||
accumulate();
|
||||
if (ntimestep % nfreq) return;
|
||||
|
||||
// output result to file
|
||||
evaluate();
|
||||
|
||||
if (fp && me == 0) {
|
||||
if(overwrite) fseek(fp,filepos,SEEK_SET);
|
||||
fprintf(fp,"# Timestep: " BIGINT_FORMAT "\n", ntimestep);
|
||||
for (unsigned int i=0;i<npcorr;++i) {
|
||||
fprintf(fp, "%lg ", t[i]*update->dt);
|
||||
for (unsigned int j=0;j<npair;++j) {
|
||||
fprintf(fp, "%lg ", f[j][i]);
|
||||
}
|
||||
fprintf(fp, "\n");
|
||||
}
|
||||
fflush(fp);
|
||||
if (overwrite) {
|
||||
long fileend = ftell(fp);
|
||||
if (fileend > 0) ftruncate(fileno(fp),fileend);
|
||||
}
|
||||
}
|
||||
|
||||
return;
|
||||
|
||||
}
|
||||
|
||||
void FixAveCorrelateLong::evaluate() {
|
||||
unsigned int jm=0;
|
||||
|
||||
// First correlator
|
||||
for (unsigned int j=0;j<p;++j) {
|
||||
if (ncorrelation[0][j] > 0) {
|
||||
t[jm] = j;
|
||||
for (int i=0;i<npair;++i)
|
||||
f[i][jm] = correlation[i][0][j]/ncorrelation[0][j];
|
||||
++jm;
|
||||
}
|
||||
}
|
||||
|
||||
// Subsequent correlators
|
||||
for (int k=1;k<kmax;++k) {
|
||||
for (int j=dmin;j<p;++j) {
|
||||
if (ncorrelation[k][j]>0) {
|
||||
t[jm] = j * pow((double)m, k);
|
||||
for (int i=0;i<npair;++i)
|
||||
f[i][jm] = correlation[i][k][j] / ncorrelation[k][j];
|
||||
++jm;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
npcorr = jm;
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
accumulate correlation data using more recently added values
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixAveCorrelateLong::accumulate()
|
||||
{
|
||||
int i,j,ipair;
|
||||
|
||||
//printf("DEBUG %i %i\n", nvalues, npair);
|
||||
|
||||
if (type == AUTO) {
|
||||
for (i=0; i<nvalues;i++) add(i,values[i]);
|
||||
} else if (type == UPPER) {
|
||||
ipair = 0;
|
||||
for (i=0;i<nvalues;i++)
|
||||
for (j=i+1;j<nvalues;j++) add(ipair++,values[i],values[j]);
|
||||
} else if (type == LOWER) {
|
||||
ipair = 0;
|
||||
for (i=0;i<nvalues;i++)
|
||||
for (j=0;j<i;j++) add(ipair++,values[i],values[j]);
|
||||
} else if (type == AUTOUPPER) {
|
||||
ipair = 0;
|
||||
for (i=0;i<nvalues;i++)
|
||||
for (j=i;j<nvalues;j++) {
|
||||
if (i==j) add(ipair++,values[i]);
|
||||
else add(ipair++,values[i],values[j]);
|
||||
}
|
||||
} else if (type == AUTOLOWER) {
|
||||
ipair = 0;
|
||||
for (i=0;i<nvalues;i++)
|
||||
for (j=0;j<=i;j++) {
|
||||
if (i==j) add(ipair++,values[i]);
|
||||
else add(ipair++,values[i],values[j]);
|
||||
}
|
||||
} else if (type == FULL) {
|
||||
ipair = 0;
|
||||
for (i=0;i<nvalues;i++)
|
||||
for (j=0;j<nvalues;j++) {
|
||||
if (i==j) add(ipair++,values[i]);
|
||||
else add(ipair++,values[i],values[j]);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Add a scalar value to the autocorrelator k of pair i
|
||||
------------------------------------------------------------------------- */
|
||||
void FixAveCorrelateLong::add(const int i, const double w, const unsigned int k){
|
||||
// If we exceed the correlator side, the value is discarded
|
||||
if (k == numcorrelators) return;
|
||||
if (k > kmax) kmax=k;
|
||||
|
||||
// Insert new value in shift array
|
||||
shift[i][k][insertindex[k]] = w;
|
||||
|
||||
// Add to accumulator and, if needed, add to next correlator
|
||||
accumulator[i][k] += w;
|
||||
if (i==0) ++naccumulator[k];
|
||||
if (naccumulator[k]==m) {
|
||||
add(i,accumulator[i][k]/m, k+1);
|
||||
accumulator[i][k]=0;
|
||||
if (i==npair-1) naccumulator[k]=0;
|
||||
}
|
||||
|
||||
// Calculate correlation function
|
||||
unsigned int ind1=insertindex[k];
|
||||
if (k==0) { // First correlator is different
|
||||
int ind2=ind1;
|
||||
for (unsigned int j=0;j<p;++j) {
|
||||
if (shift[i][k][ind2] > -1e10) {
|
||||
correlation[i][k][j]+= shift[i][k][ind1]*shift[i][k][ind2];
|
||||
if (i==0) ++ncorrelation[k][j];
|
||||
}
|
||||
--ind2;
|
||||
if (ind2<0) ind2+=p;
|
||||
}
|
||||
} else {
|
||||
int ind2=ind1-dmin;
|
||||
for (unsigned int j=dmin;j<p;++j) {
|
||||
if (ind2<0) ind2+=p;
|
||||
if (shift[i][k][ind2] > -1e10) {
|
||||
correlation[i][k][j]+= shift[i][k][ind1]*shift[i][k][ind2];
|
||||
if (i==0) ++ncorrelation[k][j];
|
||||
}
|
||||
--ind2;
|
||||
}
|
||||
}
|
||||
|
||||
if (i==npair-1) {
|
||||
++insertindex[k];
|
||||
if (insertindex[k]==p) insertindex[k]=0;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Add 2 scalar values to the cross-correlator k of pair i
|
||||
------------------------------------------------------------------------- */
|
||||
void FixAveCorrelateLong::add(const int i, const double wA, const double wB,
|
||||
const unsigned int k) {
|
||||
if (k == numcorrelators) return;
|
||||
if (k > kmax) kmax=k;
|
||||
|
||||
shift[i][k][insertindex[k]] = wA;
|
||||
shift2[i][k][insertindex[k]] = wB;
|
||||
|
||||
accumulator[i][k] += wA;
|
||||
accumulator2[i][k] += wB;
|
||||
if (i==0) ++naccumulator[k];
|
||||
if (naccumulator[k]==m) {
|
||||
add(i,accumulator[i][k]/m, accumulator2[i][k]/m,k+1);
|
||||
accumulator[i][k]=0;
|
||||
accumulator2[i][k]=0;
|
||||
if (i==npair-1) naccumulator[k]=0;
|
||||
}
|
||||
|
||||
unsigned int ind1=insertindex[k];
|
||||
if (k==0) {
|
||||
int ind2=ind1;
|
||||
for (unsigned int j=0;j<p;++j) {
|
||||
if (shift[i][k][ind2] > -1e10) {
|
||||
correlation[i][k][j]+= shift[i][k][ind1]*shift2[i][k][ind2];
|
||||
if (i==0) ++ncorrelation[k][j];
|
||||
}
|
||||
--ind2;
|
||||
if (ind2<0) ind2+=p;
|
||||
}
|
||||
}
|
||||
else {
|
||||
int ind2=ind1-dmin;
|
||||
for (unsigned int j=dmin;j<p;++j) {
|
||||
if (ind2<0) ind2+=p;
|
||||
if (shift[i][k][ind2] > -1e10) {
|
||||
correlation[i][k][j]+= shift[i][k][ind1]*shift2[i][k][ind2];
|
||||
if (i==0) ++ncorrelation[k][j];
|
||||
}
|
||||
--ind2;
|
||||
}
|
||||
}
|
||||
|
||||
if (i==npair-1) {
|
||||
++insertindex[k];
|
||||
if (insertindex[k]==p) insertindex[k]=0;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
nvalid = next step on which end_of_step does something
|
||||
this step if multiple of nevery, else next multiple
|
||||
startstep is lower bound
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
bigint FixAveCorrelateLong::nextvalid()
|
||||
{
|
||||
bigint nvalid = update->ntimestep;
|
||||
if (startstep > nvalid) nvalid = startstep;
|
||||
if (nvalid % nevery) nvalid = (nvalid/nevery)*nevery + nevery;
|
||||
return nvalid;
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory_usage
|
||||
------------------------------------------------------------------------- */
|
||||
double FixAveCorrelateLong::memory_usage() {
|
||||
// shift: npair x numcorrelators x p
|
||||
// shift2: npair x numcorrelators x p
|
||||
// correlation: npair x numcorrelators x p
|
||||
// accumulator: npair x numcorrelators
|
||||
// accumulator2: npair x numcorrelators
|
||||
// ncorrelation: numcorrelators x p
|
||||
// naccumulator: numcorrelators
|
||||
// insertindex: numcorrelators
|
||||
// t: numcorrelators x p
|
||||
// f: npair x numcorrelators x p
|
||||
double bytes = (4*npair*numcorrelators*p + 2*npair*numcorrelators
|
||||
+ numcorrelators*p)*sizeof(double)
|
||||
+ numcorrelators*p*sizeof(unsigned long int)
|
||||
+ 2*numcorrelators*sizeof(unsigned int);
|
||||
return bytes;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Write Restart data to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
// Save everything except t and f
|
||||
void FixAveCorrelateLong::write_restart(FILE *fp) {
|
||||
if (me == 0) {
|
||||
int nsize = 3*npair*numcorrelators*p + 2*npair*numcorrelators
|
||||
+ numcorrelators*p + 2*numcorrelators + 6;
|
||||
int n=0;
|
||||
double *list;
|
||||
memory->create(list,nsize,"correlator:list");
|
||||
list[n++]=npair;
|
||||
list[n++]=numcorrelators;
|
||||
list[n++]=p;
|
||||
list[n++]=m;
|
||||
list[n++]=nvalid;
|
||||
list[n++]=nvalid_last;
|
||||
for (int i=0;i<npair;i++)
|
||||
for (int j=0;j<numcorrelators;j++) {
|
||||
for (int k=0;k<p;k++) {
|
||||
list[n++]=shift[i][j][k];
|
||||
list[n++]=shift2[i][j][k];
|
||||
list[n++]=correlation[i][j][k];
|
||||
}
|
||||
list[n++]=accumulator[i][j];
|
||||
list[n++]=accumulator2[i][j];
|
||||
}
|
||||
for (int i=0;i<numcorrelators;i++) {
|
||||
for (int j=0;j<p;j++) list[n++]=ncorrelation[i][j];
|
||||
list[n++]=naccumulator[i];
|
||||
list[n++]=insertindex[i];
|
||||
}
|
||||
|
||||
int size = n*sizeof(double);
|
||||
fwrite(&size,sizeof(int),1,fp);
|
||||
fwrite(list,sizeof(double),n,fp);
|
||||
memory->destroy(list);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
use state info from restart file to restart the Fix
|
||||
------------------------------------------------------------------------- */
|
||||
void FixAveCorrelateLong::restart(char *buf)
|
||||
{
|
||||
int n = 0;
|
||||
double *list = (double *) buf;
|
||||
int npairin = static_cast<int> (list[n++]);
|
||||
int numcorrelatorsin = static_cast<int> (list[n++]);
|
||||
int pin = static_cast<int> (list[n++]);
|
||||
int min = static_cast<int> (list[n++]);
|
||||
nvalid = static_cast<int> (list[n++]);
|
||||
nvalid_last = static_cast<int> (list[n++]);
|
||||
|
||||
if ((npairin!=npair) || (numcorrelatorsin!=numcorrelators)
|
||||
|| (pin!=p) || (min!=m))
|
||||
error->all(FLERR,"Fix ave/correlate/long: restart and input data are different");
|
||||
|
||||
for (int i=0;i<npair;i++)
|
||||
for (int j=0;j<numcorrelators;j++) {
|
||||
for (int k=0;k<p;k++) {
|
||||
shift[i][j][k] = list[n++];
|
||||
shift2[i][j][k] = list[n++];
|
||||
correlation[i][j][k] = list[n++];
|
||||
}
|
||||
accumulator[i][j] = list[n++];
|
||||
accumulator2[i][j] = list[n++];
|
||||
}
|
||||
for (int i=0;i<numcorrelators;i++) {
|
||||
for (int j=0;j<p;j++)
|
||||
ncorrelation[i][j] = static_cast<unsigned long int>(list[n++]);
|
||||
naccumulator[i] = static_cast<unsigned int> (list[n++]);
|
||||
insertindex[i] = static_cast<unsigned int> (list[n++]);
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user