mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1064 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
5dd0d57cb5
commit
62dd2c2e40
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@ -34,6 +34,7 @@ enum{LOWER,CENTER,UPPER,COORD};
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enum{DENSITY_MASS,DENSITY_NUM,COMPUTE,FIX};
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enum{SAMPLE,ALL};
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enum{BOX,LATTICE,REDUCED};
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enum{ONE,RUNNING,WINDOW};
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#define BIG 1000000000
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@ -42,7 +43,7 @@ enum{BOX,LATTICE,REDUCED};
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FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg < 12) error->all("Illegal fix ave/spatial command");
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if (narg < 11) error->all("Illegal fix ave/spatial command");
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MPI_Comm_rank(world,&me);
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@ -65,38 +66,30 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
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delta = atof(arg[8]);
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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/spatial file %s",arg[9]);
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error->one(str);
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}
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}
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if (strcmp(arg[10],"density") == 0) {
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if (strcmp(arg[11],"mass") == 0) which = DENSITY_MASS;
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else if (strcmp(arg[11],"number") == 0) which = DENSITY_NUM;
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if (strcmp(arg[9],"density") == 0) {
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if (strcmp(arg[10],"mass") == 0) which = DENSITY_MASS;
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else if (strcmp(arg[10],"number") == 0) which = DENSITY_NUM;
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else error->all("Illegal fix ave/spatial command");
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} else if (strcmp(arg[10],"compute") == 0) {
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} else if (strcmp(arg[9],"compute") == 0) {
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which = COMPUTE;
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int n = strlen(arg[11]) + 1;
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int n = strlen(arg[10]) + 1;
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id_compute = new char[n];
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strcpy(id_compute,arg[11]);
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} else if (strcmp(arg[10],"fix") == 0) {
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strcpy(id_compute,arg[10]);
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} else if (strcmp(arg[9],"fix") == 0) {
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which = FIX;
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int n = strlen(arg[11]) + 1;
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int n = strlen(arg[10]) + 1;
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id_fix = new char[n];
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strcpy(id_fix,arg[11]);
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strcpy(id_fix,arg[10]);
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} else error->all("Illegal fix ave/spatial command");
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// parse optional args
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normflag = ALL;
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scaleflag = BOX;
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fp = NULL;
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ave = ONE;
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int iarg = 12;
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int iarg = 11;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"norm") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
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@ -111,6 +104,30 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
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else if (strcmp(arg[iarg+1],"reduced") == 0) scaleflag = REDUCED;
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else error->all("Illegal fix ave/spatial 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/spatial 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/spatial 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/spatial 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/spatial command");
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if (ave == WINDOW) {
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if (iarg+3 > narg) error->all("Illegal fix ave/spatial command");
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nwindow = atoi(arg[iarg+2]);
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if (nwindow <= 0) error->all("Illegal fix ave/spatial 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/spatial command");
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}
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@ -191,26 +208,35 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
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fprintf(fp,"Layer Coord Atoms Value(s) (one per layer)\n");
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}
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nlayers = maxlayer = 0;
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coord = NULL;
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count_one = count_many = count_total = NULL;
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values_one = values_many = values_total = NULL;
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// enable this fix to produce a global vector
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// set size_vector to BIG since compute_vector() will check bounds
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// no need to initialize vector to 0.0, since compute_vector() returns 0.0
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vector_flag = 1;
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size_vector = BIG;
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scalar_vector_freq = nfreq;
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extensive = 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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nlayers = maxlayer = 0;
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coord = NULL;
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count_one = count_many = count_sum = NULL;
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count_list = NULL;
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values_one = values_many = values_sum = values_total = NULL;
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values_list = NULL;
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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/spatial cannot be started on this timestep");
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}
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@ -227,10 +253,14 @@ FixAveSpatial::~FixAveSpatial()
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memory->sfree(coord);
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memory->sfree(count_one);
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memory->sfree(count_many);
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memory->sfree(count_sum);
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memory->sfree(count_total);
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memory->destroy_2d_double_array(count_list);
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memory->destroy_2d_double_array(values_one);
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memory->destroy_2d_double_array(values_many);
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memory->destroy_2d_double_array(values_sum);
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memory->destroy_2d_double_array(values_total);
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memory->destroy_3d_double_array(values_list);
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}
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/* ---------------------------------------------------------------------- */
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@ -246,6 +276,13 @@ int FixAveSpatial::setmask()
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void FixAveSpatial::init()
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{
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// # of layers cannot vary for ave = RUNNING or WINDOW
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if (ave == RUNNING || ave == WINDOW) {
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if (scaleflag != REDUCED && domain->box_change)
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error->all("Fix ave/spatial settings invalid with changing box");
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}
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// set ptrs to one or more computes called each end-of-step
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if (which == COMPUTE) {
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@ -278,6 +315,15 @@ void FixAveSpatial::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 FixAveSpatial::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 FixAveSpatial::end_of_step()
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@ -343,20 +389,45 @@ void FixAveSpatial::end_of_step()
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count_many = (double *)
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memory->srealloc(count_many,nlayers*sizeof(double),
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"ave/spatial:count_many");
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count_sum = (double *)
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memory->srealloc(count_sum,nlayers*sizeof(double),
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"ave/spatial:count_sum");
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count_total = (double *)
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memory->srealloc(count_total,nlayers*sizeof(double),
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"ave/spatial:count_total");
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values_one = memory->grow_2d_double_array(values_one,nlayers,nvalues,
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"ave/spatial:values_one");
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values_many = memory->grow_2d_double_array(values_many,nlayers,nvalues,
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"ave/spatial:values_many");
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values_sum = memory->grow_2d_double_array(values_sum,nlayers,nvalues,
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"ave/spatial:values_sum");
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values_total = memory->grow_2d_double_array(values_total,nlayers,nvalues,
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"ave/spatial:values_total");
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"ave/spatial:values_total");
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// initialize count and values total to zero since they accumulate
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for (m = 0; m < nlayers; m++) {
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for (i = 0; i < nvalues; i++) values_total[m][i] = 0.0;
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count_total[m] = 0.0;
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}
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// only allocate count and values list for ave = RUNNING or WINDOW
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// only happens once since nlayers never changes for these ave settings
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if (ave == RUNNING || ave == WINDOW) {
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count_list =
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memory->create_2d_double_array(nwindow,nlayers,
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"ave/spatial:count_list");
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values_list =
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memory->create_3d_double_array(nwindow,nlayers,nvalues,
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"ave/spatial:values_list");
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}
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}
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for (m = 0; m < nlayers; m++) {
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coord[m] = offset + (m+0.5)*delta;
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count_many[m] = count_total[m] = 0.0;
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count_many[m] = count_sum[m] = 0.0;
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for (i = 0; i < nvalues; i++) values_many[m][i] = 0.0;
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}
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}
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@ -481,66 +552,108 @@ void FixAveSpatial::end_of_step()
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if (count_many[m] > 0.0)
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for (j = 0; j < nvalues; j++)
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values_many[m][j] += values_one[m][j]/count_many[m];
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count_total[m] += count_many[m];
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count_sum[m] += count_many[m];
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}
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}
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// update counters
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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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// time average across samples
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// if density, also normalize by volume
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double repeat = nrepeat;
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if (normflag == ALL) {
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MPI_Allreduce(count_many,count_sum,nlayers,MPI_DOUBLE,MPI_SUM,world);
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MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nlayers*nvalues,
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MPI_DOUBLE,MPI_SUM,world);
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for (m = 0; m < nlayers; m++) {
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if (count_sum[m] > 0.0)
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for (j = 0; j < nvalues; j++)
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values_sum[m][j] /= count_sum[m];
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count_sum[m] /= repeat;
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}
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} else {
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MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nlayers*nvalues,
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MPI_DOUBLE,MPI_SUM,world);
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for (m = 0; m < nlayers; m++) {
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for (j = 0; j < nvalues; j++)
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values_sum[m][j] /= repeat;
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count_sum[m] /= repeat;
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}
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}
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if (which == DENSITY_MASS || which == DENSITY_NUM) {
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for (m = 0; m < nlayers; m++)
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values_sum[m][0] *= count_sum[m] / layer_volume;
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}
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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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irepeat = 0;
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nvalid = update->ntimestep+nfreq - (nrepeat-1)*nevery;
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if (normflag == ALL) {
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MPI_Allreduce(count_many,count_total,nlayers,MPI_DOUBLE,MPI_SUM,world);
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MPI_Allreduce(&values_many[0][0],&values_total[0][0],nlayers*nvalues,
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MPI_DOUBLE,MPI_SUM,world);
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for (m = 0; m < nlayers; m++) {
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if (count_total[m] > 0.0)
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for (j = 0; j < nvalues; j++)
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values_total[m][j] /= count_total[m];
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count_total[m] /= repeat;
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}
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} else {
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MPI_Allreduce(&values_many[0][0],&values_total[0][0],nlayers*nvalues,
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MPI_DOUBLE,MPI_SUM,world);
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for (m = 0; m < nlayers; m++) {
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for (j = 0; j < nvalues; j++)
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values_total[m][j] /= repeat;
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count_total[m] /= repeat;
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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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for (m = 0; m < nlayers; m++) {
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for (i = 0; i < nvalues; i++)
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values_total[m][i] = values_sum[m][i];
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count_total[m] = count_sum[m];
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}
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norm = 1;
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} else if (ave == RUNNING) {
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for (m = 0; m < nlayers; m++) {
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for (i = 0; i < nvalues; i++)
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values_total[m][i] += values_sum[m][i];
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count_total[m] += count_sum[m];
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}
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norm++;
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} else if (ave == WINDOW) {
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for (m = 0; m < nlayers; m++) {
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for (i = 0; i < nvalues; i++) {
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values_total[m][i] += values_sum[m][i];
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if (window_limit) values_total[m][i] -= values_list[iwindow][m][i];
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values_list[iwindow][m][i] = values_sum[m][i];
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}
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count_total[m] += count_sum[m];
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if (window_limit) count_total[m] -= count_list[iwindow][m];
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count_list[iwindow][m] = count_sum[m];
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}
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if (which == DENSITY_MASS || which == DENSITY_NUM) {
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for (m = 0; m < nlayers; m++)
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values_total[m][0] *= count_total[m] / layer_volume;
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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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if (fp && me == 0) {
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fprintf(fp,"%d %d\n",update->ntimestep,nlayers);
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for (m = 0; m < nlayers; m++) {
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fprintf(fp," %d %g %g",m+1,coord[m],count_total[m]);
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for (i = 0; i < nvalues; i++) fprintf(fp," %g",values_total[m][i]);
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fprintf(fp,"\n");
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}
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fflush(fp);
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// output result to file
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if (fp && me == 0) {
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fprintf(fp,"%d %d\n",update->ntimestep,nlayers);
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for (m = 0; m < nlayers; m++) {
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fprintf(fp," %d %g %g",m+1,coord[m],count_total[m]/norm);
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for (i = 0; i < nvalues; i++) fprintf(fp," %g",values_total[m][i]/norm);
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fprintf(fp,"\n");
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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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}
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fflush(fp);
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}
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}
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/* ----------------------------------------------------------------------
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return Nth vector value
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since values_total is 2d array, map N into ilayer and ivalue
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since values_sum is 2d array, map N into ilayer and ivalue
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if ilayer >= nlayers, just return 0, since nlayers can vary with time
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------------------------------------------------------------------------- */
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@ -548,6 +661,6 @@ double FixAveSpatial::compute_vector(int n)
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{
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int ivalue = n % nvalues;
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int ilayer = n / nvalues;
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if (ilayer < nlayers) return values_total[ilayer][ivalue];
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if (ilayer < nlayers && norm) return values_total[ilayer][ivalue]/norm;
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return 0.0;
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}
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@ -25,6 +25,7 @@ class FixAveSpatial : public Fix {
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~FixAveSpatial();
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int setmask();
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void init();
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void setup();
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void end_of_step();
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double compute_vector(int);
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@ -36,16 +37,23 @@ class FixAveSpatial : public Fix {
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char *id_compute,*id_fix;
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FILE *fp;
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int nlayers,nvalues,maxlayer,scaleflag,size_peratom;
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int nlayers,nvalues,ave,nwindow;
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int maxlayer,scaleflag,size_peratom;
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double xscale,yscale,zscale;
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double layer_volume;
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double *coord;
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double *count_one,*count_many,*count_total;
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double **values_one,**values_many,**values_total;
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double *count_one,*count_many,*count_sum;
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double **values_one,**values_many,**values_sum;
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double offset,invdelta;
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int ncompute;
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class Compute **compute;
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class Fix *fix;
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||||
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int norm,iwindow,window_limit;
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double *count_total;
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double **count_list;
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double **values_total;
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||||
double ***values_list;
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};
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||||
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}
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||||
|
|
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|||
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|
@ -164,7 +164,6 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
|
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else size_vector = modify->fix[ifix]->size_vector;
|
||||
vector = new double[size_vector];
|
||||
vector_total = new double[size_vector];
|
||||
for (int i = 0; i < size_vector; i++) vector_total[i] = 0.0;
|
||||
}
|
||||
|
||||
scalar_list = NULL;
|
||||
|
|
@ -172,7 +171,7 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
|
|||
if (sflag && ave == WINDOW) scalar_list = new double[nwindow];
|
||||
if (vflag && ave == WINDOW)
|
||||
vector_list = memory->create_2d_double_array(nwindow,size_vector,
|
||||
"fix ave/time:vector_list");
|
||||
"ave/time:vector_list");
|
||||
|
||||
// enable this fix to produce a global scalar and/or vector
|
||||
|
||||
|
|
@ -183,10 +182,13 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
|
|||
else extensive = modify->fix[ifix]->extensive;
|
||||
|
||||
// initializations
|
||||
// set scalar and vector total to zero since they accumulate
|
||||
|
||||
irepeat = 0;
|
||||
iwindow = window_limit = 0;
|
||||
norm = 0;
|
||||
scalar_total = 0.0;
|
||||
if (vflag) for (int i = 0; i < size_vector; i++) vector_total[i] = 0.0;
|
||||
|
||||
// nvalid = next step on which end_of_step does something
|
||||
// can be this timestep if multiple of nfreq and nrepeat = 1
|
||||
|
|
@ -315,12 +317,13 @@ void FixAveTime::end_of_step()
|
|||
if (irepeat < nrepeat) return;
|
||||
|
||||
// average the final result for the Nfreq timestep
|
||||
// reset irepeat and nvalid
|
||||
|
||||
double repeat = nrepeat;
|
||||
if (sflag) scalar /= repeat;
|
||||
if (vflag) for (i = 0; i < size_vector; i++) vector[i] /= repeat;
|
||||
|
||||
// reset irepeat and nvalid
|
||||
|
||||
irepeat = 0;
|
||||
nvalid = update->ntimestep+nfreq - (nrepeat-1)*nevery;
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue