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Copy pathoutput.cpp
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718 lines (576 loc) · 18.1 KB
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/* ----------------------------------------------------------------------
miniMD is a simple, parallel molecular dynamics (MD) code. miniMD is
an MD microapplication in the Mantevo project at Sandia National
Laboratories ( http://www.mantevo.org ). The primary
authors of miniMD are Steve Plimpton (sjplimp@sandia.gov), Paul Crozier
(pscrozi@sandia.gov) and Christian Trott (crtrott@sandia.gov).
Copyright (2008) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This library is free software; you
can redistribute it and/or modify it under the terms of the GNU Lesser
General Public License as published by the Free Software Foundation;
either version 3 of the License, or (at your option) any later
version.
This library is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this software; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
USA. See also: http://www.gnu.org/licenses/lgpl.txt .
For questions, contact Paul S. Crozier (pscrozi@sandia.gov) or
Christian Trott (crtrott@sandia.gov).
Please read the accompanying README and LICENSE files.
---------------------------------------------------------------------- */
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "integrate.h"
#include "ljs.h"
#include "miniMD_math.h"
#include "mpi.h"
#include "neighbor.h"
#include "stdio.h"
#include "stdlib.h"
#include "thermo.h"
#include "timer.h"
#include "variant.h"
#include <time.h>
void stats(int, double *, double *, double *, double *, int, int *);
void output(In &in, Atom &atom, Force *force, Neighbor &neighbor, Comm &comm, Thermo &thermo, Integrate &integrate, Timer &timer, int screen_yaml)
{
int i, n;
int me, nprocs;
int histo[10];
double tmp, ave, max, min, total;
FILE * fp;
MPI_Comm_rank(MPI_COMM_WORLD, &me);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
/* enforce PBC, then check for lost atoms */
atom.pbc();
int natoms;
MPI_Allreduce(&atom.nlocal, &natoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
int nlost = 0;
for(i = 0; i < atom.nlocal; i++)
{
if(atom.x[i * PAD + 0] < 0.0 || atom.x[i * PAD + 0] >= atom.box.xprd || atom.x[i * PAD + 1] < 0.0 || atom.x[i * PAD + 1] >= atom.box.yprd || atom.x[i * PAD + 2] < 0.0 || atom.x[i * PAD + 2] >= atom.box.zprd)
{
nlost++;
}
}
int nlostall;
MPI_Allreduce(&nlost, &nlostall, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
if(natoms != atom.natoms || nlostall > 0)
{
if(me == 0)
{
printf("Atom counts = %d %d %d\n", nlostall, natoms, atom.natoms);
}
if(me == 0)
{
printf("ERROR: Incorrect number of atoms\n");
}
return;
}
/* long-range energy and pressure corrections Whats this???*/
double engcorr = 8.0 * 3.1415926 * in.rho * (1.0 / (9.0 * pow(force->cutforce, MMD_float(9.0))) - 1.0 / (3.0 * pow(force->cutforce, MMD_float(3.0))));
double prscorr = 8.0 * 3.1415926 * in.rho * in.rho * (4.0 / (9.0 * pow(force->cutforce, MMD_float(9.0))) - 2.0 / (3.0 * pow(force->cutforce, MMD_float(3.0))));
/* thermo output */
double conserve;
if(me == 0)
{
time_t general_time = time(NULL);
struct tm local_time = *localtime(&general_time);
char filename[256];
sprintf(filename, "miniMD-%4d-%02d-%02d-%02d-%02d-%02d.yaml", local_time.tm_year + 1900, local_time.tm_mon + 1, local_time.tm_mday, local_time.tm_hour, local_time.tm_min, local_time.tm_sec);
fp = fopen(filename, "w");
if(screen_yaml)
{
fprintf(stdout, "run_configuration: \n");
fprintf(stdout, " variant: " VARIANT_STRING "\n");
fprintf(stdout, " mpi_processes: %i\n", neighbor.threads->mpi_num_threads);
fprintf(stdout, " thread_teams: %i\n", neighbor.threads->teams);
fprintf(stdout, " threads: %i\n", neighbor.threads->omp_num_threads);
fprintf(stdout, " datafile: %s\n", in.datafile ? in.datafile : "None");
fprintf(stdout, " units: %s\n", in.units == 0 ? "LJ" : "METAL");
fprintf(stdout, " atoms: %i\n", atom.natoms);
fprintf(stdout, " atom_types: %i\n", atom.ntypes);
fprintf(stdout, " system_size: %2.2lf %2.2lf %2.2lf\n", atom.box.xprd, atom.box.yprd, atom.box.zprd);
fprintf(stdout, " unit_cells: %i %i %i\n", in.nx, in.ny, in.nz);
fprintf(stdout, " density: %lf\n", in.rho);
fprintf(stdout, " force_type: %s\n", in.forcetype == FORCELJ ? "LJ" : "EAM");
fprintf(stdout, " force_cutoff: %lf\n", force->cutforce);
fprintf(stdout, " force_params: %2.2lf %2.2lf\n", ( double )*force->epsilon, ( double )*force->sigma);
fprintf(stdout, " neighbor_cutoff: %lf\n", neighbor.cutneigh);
fprintf(stdout, " neighbor_type: %i\n", neighbor.halfneigh);
fprintf(stdout, " neighbor_bins: %i %i %i\n", neighbor.nbinx, neighbor.nbiny, neighbor.nbinz);
fprintf(stdout, " neighbor_frequency: %i\n", neighbor.every);
fprintf(stdout, " sort_frequency: %i\n", integrate.sort_every);
fprintf(stdout, " timestep_size: %lf\n", integrate.dt);
fprintf(stdout, " thermo_frequency: %i\n", thermo.nstat);
fprintf(stdout, " ghost_newton: %i\n", neighbor.ghost_newton);
fprintf(stdout, " use_intrinsics: %i\n", force->use_sse);
fprintf(stdout, " safe_exchange: %i\n", comm.do_safeexchange);
fprintf(stdout, " float_size: %i\n\n", ( int )sizeof(MMD_float));
}
fprintf(fp, "run_configuration: \n");
fprintf(fp, " variant: " VARIANT_STRING "\n");
fprintf(fp, " mpi_processes: %i\n", neighbor.threads->mpi_num_threads);
fprintf(fp, " thread_teams: %i\n", neighbor.threads->teams);
fprintf(fp, " threads: %i\n", neighbor.threads->omp_num_threads);
fprintf(fp, " datafile: %s\n", in.datafile ? in.datafile : "None");
fprintf(fp, " units: %s\n", in.units == 0 ? "LJ" : "METAL");
fprintf(fp, " atoms: %i\n", atom.natoms);
fprintf(fp, " atom_types: %i\n", atom.ntypes);
fprintf(fp, " system_size: %2.2lf %2.2lf %2.2lf\n", atom.box.xprd, atom.box.yprd, atom.box.zprd);
fprintf(fp, " unit_cells: %i %i %i\n", in.nx, in.ny, in.nz);
fprintf(fp, " density: %lf\n", in.rho);
fprintf(fp, " force_type: %s\n", in.forcetype == FORCELJ ? "LJ" : "EAM");
fprintf(fp, " force_cutoff: %lf\n", force->cutforce);
fprintf(fp, " force_params: %2.2lf %2.2lf\n", ( double )*force->epsilon, ( double )*force->sigma);
fprintf(fp, " neighbor_cutoff: %lf\n", neighbor.cutneigh);
fprintf(fp, " neighbor_type: %i\n", neighbor.halfneigh);
fprintf(fp, " neighbor_bins: %i %i %i\n", neighbor.nbinx, neighbor.nbiny, neighbor.nbinz);
fprintf(fp, " neighbor_frequency: %i\n", neighbor.every);
fprintf(fp, " sort_frequency: %i\n", integrate.sort_every);
fprintf(fp, " timestep_size: %lf\n", integrate.dt);
fprintf(fp, " thermo_frequency: %i\n", thermo.nstat);
fprintf(fp, " ghost_newton: %i\n", neighbor.ghost_newton);
fprintf(fp, " use_intrinsics: %i\n", force->use_sse);
fprintf(fp, " safe_exchange: %i\n", comm.do_safeexchange);
fprintf(fp, " float_size: %i\n\n", ( int )sizeof(MMD_float));
if(screen_yaml)
{
fprintf(stdout, "\n\nthermodynamic_output:\n");
}
fprintf(fp, "\n\nthermodynamic_output:\n");
for(i = 0; i < thermo.mstat; i++)
{
conserve = (1.5 * thermo.tmparr[i] + thermo.engarr[i]) / (1.5 * thermo.tmparr[0] + thermo.engarr[0]);
if(screen_yaml)
{
fprintf(stdout, " timestep: %d \n", thermo.steparr[i]);
fprintf(stdout, " T*: %15.10g \n", thermo.tmparr[i]);
// fprintf(stdout," U*: %15.10g \n", thermo.engarr[i]+engcorr);
// fprintf(stdout," P*: %15.10g \n", thermo.prsarr[i]+prscorr);
fprintf(stdout, " U*: %15.10g \n", thermo.engarr[i]);
fprintf(stdout, " P*: %15.10g \n", thermo.prsarr[i]);
fprintf(stdout, " Conservation: %15.10g \n", conserve);
}
fprintf(fp, " timestep: %d \n", thermo.steparr[i]);
fprintf(fp, " T*: %15.10g \n", thermo.tmparr[i]);
// fprintf(fp ," U*: %15.10g \n", thermo.engarr[i]+engcorr);
// fprintf(fp ," P*: %15.10g \n", thermo.prsarr[i]+prscorr);
fprintf(fp, " U*: %15.10g \n", thermo.engarr[i]);
fprintf(fp, " P*: %15.10g \n", thermo.prsarr[i]);
fprintf(fp, " Conservation: %15.10g \n", conserve);
}
}
/* performance output */
if(me == 0)
{
fprintf(stdout, "\n\n");
fprintf(fp, "\n\n");
}
double time_total = timer.array[TIME_TOTAL];
MPI_Allreduce(&time_total, &tmp, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
time_total = tmp / nprocs;
double mflops = 4.0 / 3.0 * 3.1415926 * pow(force->cutforce, MMD_float(3.0)) * in.rho * 0.5 * 23 * natoms * integrate.ntimes / time_total / 1000000.0;
if(me == 0)
{
if(screen_yaml)
{
fprintf(stdout, "time:\n");
fprintf(stdout, " total:\n");
fprintf(stdout, " time: %g \n", time_total);
fprintf(stdout, " performance: %10.5e \n", natoms * integrate.ntimes / time_total);
fprintf(stdout, " performance_proc: %10.5e \n", natoms * integrate.ntimes / time_total / neighbor.threads->mpi_num_threads / neighbor.threads->omp_num_threads);
}
fprintf(fp, "time:\n");
fprintf(fp, " total:\n");
fprintf(fp, " time: %g \n", time_total);
fprintf(fp, " performance: %10.5e \n", natoms * integrate.ntimes / time_total);
fprintf(fp, " performance_proc: %10.5e \n", natoms * integrate.ntimes / time_total / neighbor.threads->mpi_num_threads / neighbor.threads->omp_num_threads);
}
if(time_total == 0.0)
{
time_total = 1.0;
}
double time_force = timer.array[TIME_FORCE];
MPI_Allreduce(&time_force, &tmp, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
tmp /= nprocs;
if(me == 0)
{
if(screen_yaml)
{
fprintf(stdout, " force: %g\n", tmp);
}
fprintf(fp, " force: %g\n", tmp);
}
double time_neigh = timer.array[TIME_NEIGH];
MPI_Allreduce(&time_neigh, &tmp, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
tmp /= nprocs;
if(me == 0)
{
if(screen_yaml)
{
fprintf(stdout, " neigh: %g\n", tmp);
}
fprintf(fp, " neigh: %g\n", tmp);
}
double time_comm = timer.array[TIME_COMM];
MPI_Allreduce(&time_comm, &tmp, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
tmp /= nprocs;
if(me == 0)
{
if(screen_yaml)
{
fprintf(stdout, " comm: %g\n", tmp);
}
fprintf(fp, " comm: %g\n", tmp);
}
double time_other = time_total - (time_force + time_neigh + time_comm);
MPI_Allreduce(&time_other, &tmp, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
tmp /= nprocs;
if(me == 0)
{
if(screen_yaml)
{
fprintf(stdout, " other: %g\n", tmp);
}
fprintf(fp, " other: %g\n", tmp);
}
if(me == 0)
{
if(screen_yaml)
{
fprintf(stdout, "\n");
}
fprintf(fp, "\n");
}
stats(1, &time_force, &ave, &max, &min, 10, histo);
if(me == 0)
{
if(screen_yaml)
{
fprintf(stdout, "# Timing histograms \n");
fprintf(stdout, "# Force time: %g ave %g max %g min\n", ave, max, min);
fprintf(stdout, "# Histogram:");
for(i = 0; i < 10; i++)
{
fprintf(stdout, " %d", histo[i]);
}
fprintf(stdout, "\n");
}
fprintf(fp, "# Timing histograms \n");
fprintf(fp, "# Force time: %g ave %g max %g min\n", ave, max, min);
fprintf(fp, "# Histogram:");
for(i = 0; i < 10; i++)
{
fprintf(fp, " %d", histo[i]);
}
fprintf(fp, "\n");
}
stats(1, &time_neigh, &ave, &max, &min, 10, histo);
if(me == 0)
{
if(screen_yaml)
{
fprintf(stdout, "# Neigh time: %g ave %g max %g min\n", ave, max, min);
fprintf(stdout, "# Histogram:");
for(i = 0; i < 10; i++)
{
fprintf(stdout, " %d", histo[i]);
}
fprintf(stdout, "\n");
}
fprintf(fp, "# Neigh time: %g ave %g max %g min\n", ave, max, min);
fprintf(fp, "# Histogram:");
for(i = 0; i < 10; i++)
{
fprintf(fp, " %d", histo[i]);
}
fprintf(fp, "\n");
}
stats(1, &time_comm, &ave, &max, &min, 10, histo);
if(me == 0)
{
if(screen_yaml)
{
fprintf(stdout, "# Comm time: %g ave %g max %g min\n", ave, max, min);
}
if(screen_yaml)
{
fprintf(stdout, "# Histogram:");
}
if(screen_yaml)
{
for(i = 0; i < 10; i++)
{
fprintf(stdout, " %d", histo[i]);
}
}
if(screen_yaml)
{
fprintf(stdout, "\n");
}
fprintf(fp, "# Comm time: %g ave %g max %g min\n", ave, max, min);
fprintf(fp, "# Histogram:");
for(i = 0; i < 10; i++)
{
fprintf(fp, " %d", histo[i]);
}
fprintf(fp, "\n");
}
stats(1, &time_other, &ave, &max, &min, 10, histo);
if(me == 0)
{
if(screen_yaml)
{
fprintf(stdout, "# Other time: %g ave %g max %g min\n", ave, max, min);
}
if(screen_yaml)
{
fprintf(stdout, "# Histogram:");
}
if(screen_yaml)
{
for(i = 0; i < 10; i++)
{
fprintf(stdout, " %d", histo[i]);
}
}
if(screen_yaml)
{
fprintf(stdout, "\n");
}
fprintf(fp, "# Other time: %g ave %g max %g min\n", ave, max, min);
fprintf(fp, "# Histogram:");
for(i = 0; i < 10; i++)
{
fprintf(fp, " %d", histo[i]);
}
fprintf(fp, "\n");
}
if(me == 0)
{
fprintf(stdout, "\n");
fprintf(fp, "\n");
}
tmp = atom.nlocal;
stats(1, &tmp, &ave, &max, &min, 10, histo);
if(me == 0)
{
if(screen_yaml)
{
fprintf(stdout, "# Nlocal: %g ave %g max %g min\n", ave, max, min);
}
if(screen_yaml)
{
fprintf(stdout, "# Histogram:");
}
if(screen_yaml)
{
for(i = 0; i < 10; i++)
{
fprintf(stdout, " %d", histo[i]);
}
}
if(screen_yaml)
{
fprintf(stdout, "\n");
}
fprintf(fp, "# Nlocal: %g ave %g max %g min\n", ave, max, min);
fprintf(fp, "# Histogram:");
for(i = 0; i < 10; i++)
{
fprintf(fp, " %d", histo[i]);
}
fprintf(fp, "\n");
}
tmp = atom.nghost;
stats(1, &tmp, &ave, &max, &min, 10, histo);
if(me == 0)
{
if(screen_yaml)
{
fprintf(stdout, "# Nghost: %g ave %g max %g min\n", ave, max, min);
}
if(screen_yaml)
{
fprintf(stdout, "# Histogram:");
}
if(screen_yaml)
{
for(i = 0; i < 10; i++)
{
fprintf(stdout, " %d", histo[i]);
}
}
if(screen_yaml)
{
fprintf(stdout, "\n");
}
fprintf(fp, "# Nghost: %g ave %g max %g min\n", ave, max, min);
fprintf(fp, "# Histogram:");
for(i = 0; i < 10; i++)
{
fprintf(fp, " %d", histo[i]);
}
fprintf(fp, "\n");
}
n = 0;
for(i = 0; i < comm.nswap; i++)
{
n += comm.sendnum[i];
}
tmp = n;
stats(1, &tmp, &ave, &max, &min, 10, histo);
if(me == 0)
{
if(screen_yaml)
{
fprintf(stdout, "# Nswaps: %g ave %g max %g min\n", ave, max, min);
}
if(screen_yaml)
{
fprintf(stdout, "# Histogram:");
}
if(screen_yaml)
{
for(i = 0; i < 10; i++)
{
fprintf(stdout, " %d", histo[i]);
}
}
if(screen_yaml)
{
fprintf(stdout, "\n");
}
fprintf(fp, "# Nswaps: %g ave %g max %g min\n", ave, max, min);
fprintf(fp, "# Histogram:");
for(i = 0; i < 10; i++)
{
fprintf(fp, " %d", histo[i]);
}
fprintf(fp, "\n");
}
n = 0;
for(i = 0; i < atom.nlocal; i++)
{
n += neighbor.numneigh[i];
}
tmp = n;
stats(1, &tmp, &ave, &max, &min, 10, histo);
if(me == 0)
{
if(screen_yaml)
{
fprintf(stdout, "# Neighs: %g ave %g max %g min\n", ave, max, min);
}
if(screen_yaml)
{
fprintf(stdout, "# Histogram:");
}
if(screen_yaml)
{
for(i = 0; i < 10; i++)
{
fprintf(stdout, " %d", histo[i]);
}
}
if(screen_yaml)
{
fprintf(stdout, "\n");
}
fprintf(fp, "# Neighs: %g ave %g max %g min\n", ave, max, min);
fprintf(fp, "# Histogram:");
for(i = 0; i < 10; i++)
{
fprintf(fp, " %d", histo[i]);
}
fprintf(fp, "\n");
}
MPI_Allreduce(&tmp, &total, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
if(me == 0)
{
if(screen_yaml)
{
fprintf(stdout, "# Total # of neighbors = %g\n", total);
}
fprintf(fp, "# Total # of neighbors = %g\n", total);
}
if(me == 0)
{
if(screen_yaml)
{
fprintf(stdout, "\n");
}
fprintf(fp, "\n");
}
if(me == 0)
{
fclose(fp);
}
}
void stats(int n, double *data, double *pave, double *pmax, double *pmin, int nhisto, int *histo)
{
int i, m;
int *histotmp;
double min = 1.0e20;
double max = -1.0e20;
double ave = 0.0;
for(i = 0; i < n; i++)
{
ave += data[i];
if(data[i] < min)
{
min = data[i];
}
if(data[i] > max)
{
max = data[i];
}
}
int ntotal;
MPI_Allreduce(&n, &ntotal, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
double tmp;
MPI_Allreduce(&ave, &tmp, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
ave = tmp / ntotal;
MPI_Allreduce(&min, &tmp, 1, MPI_DOUBLE, MPI_MIN, MPI_COMM_WORLD);
min = tmp;
MPI_Allreduce(&max, &tmp, 1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD);
max = tmp;
for(i = 0; i < nhisto; i++)
{
histo[i] = 0;
}
double del = max - min;
for(i = 0; i < n; i++)
{
if(del == 0.0)
{
m = 0;
}
else
{
m = static_cast<int>((data[i] - min) / del * nhisto);
}
if(m > nhisto - 1)
{
m = nhisto - 1;
}
histo[m]++;
}
histotmp = ( int * )malloc(nhisto * sizeof(int));
MPI_Allreduce(histo, histotmp, nhisto, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
for(i = 0; i < nhisto; i++)
{
histo[i] = histotmp[i];
}
free(histotmp);
*pave = ave;
*pmax = max;
*pmin = min;
}