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lammps
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3117 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-08-21 19:05:42 +00:00
parent e5e065628d
commit c01b4e016c
17 changed files with 580 additions and 267 deletions
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539
src/finish.cpp
View File

@ -38,53 +38,76 @@ Finish::Finish(LAMMPS *lmp) : Pointers(lmp) {}
void Finish::end(int flag)
{
int i,m;
int i,m,nneigh;
int histo[10];
double time,tmp,ave,max,min;
int loopflag,minflag,prdflag,timeflag,fftflag,histoflag,neighflag;
double time,tmp,ave,max,min,natoms;
double time_loop,time_other;
int me,nprocs;
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
// deduce time_other
// choose flavors of statistical output
// flag determines caller
// flag = 0 = just loop summary
// flag = 1 = dynamics or minimization
// flag = 2 = PRD
loopflag = 1;
minflag = prdflag = timeflag = fftflag = histoflag = neighflag = 0;
double time_other = timer->array[TIME_LOOP] -
(timer->array[TIME_PAIR] + timer->array[TIME_BOND] +
timer->array[TIME_KSPACE] + timer->array[TIME_NEIGHBOR] +
timer->array[TIME_COMM] + timer->array[TIME_OUTPUT]);
double time_loop = timer->array[TIME_LOOP];
MPI_Allreduce(&time_loop,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time_loop = tmp/nprocs;
// overall loop time
// use actual natoms, in case atoms were lost
double natoms;
double rlocal = atom->nlocal;
MPI_Allreduce(&rlocal,&natoms,1,MPI_DOUBLE,MPI_SUM,world);
if (me == 0) {
if (screen)
fprintf(screen,
"Loop time of %g on %d procs for %d steps with %.15g atoms\n",
time_loop,nprocs,update->nsteps,natoms);
if (logfile)
fprintf(logfile,
"Loop time of %g on %d procs for %d steps with %.15g atoms\n",
time_loop,nprocs,update->nsteps,natoms);
if (flag == 1) {
if (update->whichflag == 2) minflag = 1;
timeflag = histoflag = neighflag = 1;
if (strstr(force->kspace_style,"pppm")) fftflag = 1;
}
if (flag == 2) {
prdflag = histoflag = neighflag = 1;
}
if (flag == 0) return;
// loop stats
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
if (loopflag) {
time_other = timer->array[TIME_LOOP] -
(timer->array[TIME_PAIR] + timer->array[TIME_BOND] +
timer->array[TIME_KSPACE] + timer->array[TIME_NEIGHBOR] +
timer->array[TIME_COMM] + timer->array[TIME_OUTPUT]);
time_loop = timer->array[TIME_LOOP];
MPI_Allreduce(&time_loop,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time_loop = tmp/nprocs;
// overall loop time
// use actual natoms, in case atoms were lost
natoms;
double rlocal = atom->nlocal;
MPI_Allreduce(&rlocal,&natoms,1,MPI_DOUBLE,MPI_SUM,world);
if (me == 0) {
if (screen)
fprintf(screen,
"Loop time of %g on %d procs for %d steps with %.15g atoms\n",
time_loop,nprocs,update->nsteps,natoms);
if (logfile)
fprintf(logfile,
"Loop time of %g on %d procs for %d steps with %.15g atoms\n",
time_loop,nprocs,update->nsteps,natoms);
}
if (time_loop == 0.0) time_loop = 1.0;
}
// minimization stats
if (update->whichflag == 2) {
if (minflag) {
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
if (me == 0) {
if (screen) {
fprintf(screen,"Minimization stats:\n");
@ -127,98 +150,170 @@ void Finish::end(int flag)
update->minimize->niter,update->minimize->neval);
}
}
}
// PRD stats using PAIR,BOND,KSPACE for dephase,dynamics,quench
if (prdflag) {
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
}
// timing breakdowns
if (screen) fprintf(screen,"PRD stats:\n");
if (logfile) fprintf(logfile,"PRD stats:\n");
if (time_loop == 0.0) time_loop = 1.0;
time = timer->array[TIME_PAIR];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen," Dephase time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile," Dephase time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
time = timer->array[TIME_PAIR];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Pair time (%%) = %g (%g)\n",time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Pair time (%%) = %g (%g)\n",time,time/time_loop*100.0);
}
if (atom->molecular) {
time = timer->array[TIME_BOND];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Bond time (%%) = %g (%g)\n",
fprintf(screen," Dynamics time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Bond time (%%) = %g (%g)\n",
if (logfile)
fprintf(logfile," Dynamics time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
}
if (force->kspace) {
time = timer->array[TIME_KSPACE];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Kspce time (%%) = %g (%g)\n",
fprintf(screen," Quench time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Kspce time (%%) = %g (%g)\n",
if (logfile)
fprintf(logfile," Quench time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
time = time_other;
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen," Other time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile," Other time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
}
time = timer->array[TIME_NEIGHBOR];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Neigh time (%%) = %g (%g)\n",time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Neigh time (%%) = %g (%g)\n",time,time/time_loop*100.0);
}
// timing breakdowns
time = timer->array[TIME_COMM];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Comm time (%%) = %g (%g)\n",time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Comm time (%%) = %g (%g)\n",time,time/time_loop*100.0);
}
if (timeflag) {
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
time = timer->array[TIME_OUTPUT];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Outpt time (%%) = %g (%g)\n",time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Outpt time (%%) = %g (%g)\n",time,time/time_loop*100.0);
}
time = timer->array[TIME_PAIR];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Pair time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Pair time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
time = time_other;
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Other time (%%) = %g (%g)\n",time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Other time (%%) = %g (%g)\n",time,time/time_loop*100.0);
if (atom->molecular) {
time = timer->array[TIME_BOND];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Bond time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Bond time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
}
if (force->kspace) {
time = timer->array[TIME_KSPACE];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Kspce time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Kspce time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
}
time = timer->array[TIME_NEIGHBOR];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Neigh time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Neigh time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
time = timer->array[TIME_COMM];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Comm time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Comm time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
time = timer->array[TIME_OUTPUT];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Outpt time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Outpt time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
time = time_other;
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Other time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Other time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
}
// FFT timing statistics
// time3d,time1d = total time during run for 3d and 1d FFTs
if (strstr(force->kspace_style,"pppm")) {
if (fftflag) {
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
@ -265,151 +360,157 @@ void Finish::end(int flag)
}
}
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
tmp = atom->nlocal;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
if (screen) {
fprintf(screen,"Nlocal: %g ave %g max %g min\n",ave,max,min);
fprintf(screen,"Histogram:");
for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
fprintf(screen,"\n");
if (histoflag) {
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
if (logfile) {
fprintf(logfile,"Nlocal: %g ave %g max %g min\n",ave,max,min);
fprintf(logfile,"Histogram:");
for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
fprintf(logfile,"\n");
}
}
tmp = atom->nghost;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
if (screen) {
fprintf(screen,"Nghost: %g ave %g max %g min\n",ave,max,min);
fprintf(screen,"Histogram:");
for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
fprintf(screen,"\n");
}
if (logfile) {
fprintf(logfile,"Nghost: %g ave %g max %g min\n",ave,max,min);
fprintf(logfile,"Histogram:");
for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
fprintf(logfile,"\n");
}
}
// find a non-skip neighbor list containing half the pairwise interactions
// count neighbors in that list for stats purposes
for (m = 0; m < neighbor->old_nrequest; m++)
if ((neighbor->old_requests[m]->half || neighbor->old_requests[m]->gran ||
neighbor->old_requests[m]->respaouter ||
neighbor->old_requests[m]->half_from_full) &&
neighbor->old_requests[m]->skip == 0) break;
int nneigh = 0;
if (m < neighbor->old_nrequest) {
int inum = neighbor->lists[m]->inum;
int *ilist = neighbor->lists[m]->ilist;
int *numneigh = neighbor->lists[m]->numneigh;
for (int ii = 0; ii < inum; ii++)
nneigh += numneigh[ilist[ii]];
}
tmp = nneigh;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
if (screen) {
fprintf(screen,"Neighs: %g ave %g max %g min\n",ave,max,min);
fprintf(screen,"Histogram:");
for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
fprintf(screen,"\n");
}
if (logfile) {
fprintf(logfile,"Neighs: %g ave %g max %g min\n",ave,max,min);
fprintf(logfile,"Histogram:");
for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
fprintf(logfile,"\n");
}
}
// find a non-skip neighbor list containing full pairwise interactions
for (m = 0; m < neighbor->old_nrequest; m++)
if (neighbor->old_requests[m]->full &&
neighbor->old_requests[m]->skip == 0) break;
if (m < neighbor->old_nrequest) {
nneigh = 0;
for (i = 0; i < atom->nlocal; i++)
nneigh += neighbor->lists[m]->numneigh[i];
tmp = nneigh;
tmp = atom->nlocal;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
if (screen) {
fprintf(screen,"FullNghs: %g ave %g max %g min\n",ave,max,min);
fprintf(screen,"Nlocal: %g ave %g max %g min\n",ave,max,min);
fprintf(screen,"Histogram:");
for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
fprintf(screen,"\n");
}
if (logfile) {
fprintf(logfile,"FullNghs: %g ave %g max %g min\n",ave,max,min);
fprintf(logfile,"Nlocal: %g ave %g max %g min\n",ave,max,min);
fprintf(logfile,"Histogram:");
for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
fprintf(logfile,"\n");
}
}
}
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
tmp = nneigh;
double nall;
MPI_Allreduce(&tmp,&nall,1,MPI_DOUBLE,MPI_SUM,world);
int nspec;
double nspec_all;
if (atom->molecular) {
nspec = 0;
for (i = 0; i < atom->nlocal; i++) nspec += atom->nspecial[i][2];
tmp = nspec;
MPI_Allreduce(&tmp,&nspec_all,1,MPI_DOUBLE,MPI_SUM,world);
}
if (me == 0) {
if (screen) {
if (nall < 2.0e9)
fprintf(screen,"Total # of neighbors = %d\n",static_cast<int> (nall));
else fprintf(screen,"Total # of neighbors = %g\n",nall);
if (natoms > 0) fprintf(screen,"Ave neighs/atom = %g\n",nall/natoms);
if (atom->molecular && natoms > 0)
fprintf(screen,"Ave special neighs/atom = %g\n",nspec_all/natoms);
fprintf(screen,"Neighbor list builds = %d\n",neighbor->ncalls);
fprintf(screen,"Dangerous builds = %d\n",neighbor->ndanger);
tmp = atom->nghost;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
if (screen) {
fprintf(screen,"Nghost: %g ave %g max %g min\n",ave,max,min);
fprintf(screen,"Histogram:");
for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
fprintf(screen,"\n");
}
if (logfile) {
fprintf(logfile,"Nghost: %g ave %g max %g min\n",ave,max,min);
fprintf(logfile,"Histogram:");
for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
fprintf(logfile,"\n");
}
}
if (logfile) {
if (nall < 2.0e9)
fprintf(logfile,"Total # of neighbors = %d\n",static_cast<int> (nall));
else fprintf(logfile,"Total # of neighbors = %g\n",nall);
if (natoms > 0) fprintf(logfile,"Ave neighs/atom = %g\n",nall/natoms);
if (atom->molecular && natoms > 0)
fprintf(logfile,"Ave special neighs/atom = %g\n",nspec_all/natoms);
fprintf(logfile,"Neighbor list builds = %d\n",neighbor->ncalls);
fprintf(logfile,"Dangerous builds = %d\n",neighbor->ndanger);
// find a non-skip neighbor list containing half the pairwise interactions
// count neighbors in that list for stats purposes
for (m = 0; m < neighbor->old_nrequest; m++)
if ((neighbor->old_requests[m]->half ||
neighbor->old_requests[m]->gran ||
neighbor->old_requests[m]->respaouter ||
neighbor->old_requests[m]->half_from_full) &&
neighbor->old_requests[m]->skip == 0) break;
nneigh = 0;
if (m < neighbor->old_nrequest) {
int inum = neighbor->lists[m]->inum;
int *ilist = neighbor->lists[m]->ilist;
int *numneigh = neighbor->lists[m]->numneigh;
for (int ii = 0; ii < inum; ii++)
nneigh += numneigh[ilist[ii]];
}
tmp = nneigh;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
if (screen) {
fprintf(screen,"Neighs: %g ave %g max %g min\n",ave,max,min);
fprintf(screen,"Histogram:");
for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
fprintf(screen,"\n");
}
if (logfile) {
fprintf(logfile,"Neighs: %g ave %g max %g min\n",ave,max,min);
fprintf(logfile,"Histogram:");
for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
fprintf(logfile,"\n");
}
}
// find a non-skip neighbor list containing full pairwise interactions
for (m = 0; m < neighbor->old_nrequest; m++)
if (neighbor->old_requests[m]->full &&
neighbor->old_requests[m]->skip == 0) break;
if (m < neighbor->old_nrequest) {
nneigh = 0;
for (i = 0; i < atom->nlocal; i++)
nneigh += neighbor->lists[m]->numneigh[i];
tmp = nneigh;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
if (screen) {
fprintf(screen,"FullNghs: %g ave %g max %g min\n",ave,max,min);
fprintf(screen,"Histogram:");
for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
fprintf(screen,"\n");
}
if (logfile) {
fprintf(logfile,"FullNghs: %g ave %g max %g min\n",ave,max,min);
fprintf(logfile,"Histogram:");
for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
fprintf(logfile,"\n");
}
}
}
}
if (neighflag) {
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
tmp = nneigh;
double nall;
MPI_Allreduce(&tmp,&nall,1,MPI_DOUBLE,MPI_SUM,world);
int nspec;
double nspec_all;
if (atom->molecular) {
nspec = 0;
for (i = 0; i < atom->nlocal; i++) nspec += atom->nspecial[i][2];
tmp = nspec;
MPI_Allreduce(&tmp,&nspec_all,1,MPI_DOUBLE,MPI_SUM,world);
}
if (me == 0) {
if (screen) {
if (nall < 2.0e9)
fprintf(screen,
"Total # of neighbors = %d\n",static_cast<int> (nall));
else fprintf(screen,"Total # of neighbors = %g\n",nall);
if (natoms > 0) fprintf(screen,"Ave neighs/atom = %g\n",nall/natoms);
if (atom->molecular && natoms > 0)
fprintf(screen,"Ave special neighs/atom = %g\n",nspec_all/natoms);
fprintf(screen,"Neighbor list builds = %d\n",neighbor->ncalls);
fprintf(screen,"Dangerous builds = %d\n",neighbor->ndanger);
}
if (logfile) {
if (nall < 2.0e9)
fprintf(logfile,
"Total # of neighbors = %d\n",static_cast<int> (nall));
else fprintf(logfile,"Total # of neighbors = %g\n",nall);
if (natoms > 0) fprintf(logfile,"Ave neighs/atom = %g\n",nall/natoms);
if (atom->molecular && natoms > 0)
fprintf(logfile,"Ave special neighs/atom = %g\n",nspec_all/natoms);
fprintf(logfile,"Neighbor list builds = %d\n",neighbor->ncalls);
fprintf(logfile,"Dangerous builds = %d\n",neighbor->ndanger);
}
}
}
if (logfile) fflush(logfile);
}

5
src/fix_minimize.cpp
View File

@ -181,8 +181,9 @@ double FixMinimize::memory_usage()
void FixMinimize::grow_arrays(int nmax)
{
for (int m = 0; m < nvector; m++)
vectors[m] = (double *) memory->srealloc(vectors[m],peratom[m]*nmax,
"minimize:vector");
vectors[m] = (double *)
memory->srealloc(vectors[m],peratom[m]*nmax*sizeof(double),
"minimize:vector");
}
/* ----------------------------------------------------------------------

3
src/integrate.cpp
View File

@ -79,7 +79,8 @@ void Integrate::ev_setup()
}
/* ----------------------------------------------------------------------
set eflag,vflag for current iteration with ntimestep
set eflag,vflag for current iteration
based on computes that need info on this ntimestep
eflag = 0 = no energy computation
eflag = 1 = global energy only
eflag = 2 = per-atom energy only

3
src/integrate.h
View File

@ -24,7 +24,8 @@ class Integrate : protected Pointers {
virtual ~Integrate();
virtual void init() = 0;
virtual void setup() = 0;
virtual void iterate(int) = 0;
virtual void setup_minimal(int) = 0;
virtual void run(int) = 0;
virtual void cleanup() {}
virtual void reset_dt() {}
virtual double memory_usage() {return 0.0;}

111
src/min.cpp
View File

@ -149,8 +149,6 @@ void Min::init()
neigh_delay = neighbor->delay;
neigh_dist_check = neighbor->dist_check;
// reset reneighboring criteria if necessary
if (neigh_every != 1 || neigh_delay != 0 || neigh_dist_check != 1) {
if (comm->me == 0)
error->warning("Resetting reneighboring criteria during minimization");
@ -179,6 +177,12 @@ void Min::setup()
nextra_global = modify->min_dof();
if (nextra_global) fextra = new double[nextra_global];
// compute for potential energy
int id = modify->find_compute("thermo_pe");
if (id < 0) error->all("Minimization could not find thermo_pe compute");
pe_compute = modify->compute[id];
// style-specific setup does two tasks
// setup extra global dof vectors
// setup extra per-atom dof vectors due to requests from Pair classes
@ -198,7 +202,6 @@ void Min::setup()
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
// reset gradient vector ptrs
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
@ -241,10 +244,63 @@ void Min::setup()
}
/* ----------------------------------------------------------------------
perform minimization, with setup first
setup without output or one-time post-init setup
flag = 0 = just force calculation
flag = 1 = reneighbor and force calculation
------------------------------------------------------------------------- */
void Min::run()
void Min::setup_minimal(int flag)
{
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
if (flag) {
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
neighbor->build();
neighbor->ncalls = 0;
}
// compute all forces
ev_set(update->ntimestep);
force_clear();
if (force->pair) force->pair->compute(eflag,vflag);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
}
if (force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
}
if (force->newton) comm->reverse_communicate();
modify->setup(vflag);
// atoms may have migrated in comm->exchange()
reset_vectors();
}
/* ----------------------------------------------------------------------
perform minimization, calling iterate() for nsteps
------------------------------------------------------------------------- */
void Min::run(int nsteps)
{
// possible stop conditions
@ -254,12 +310,6 @@ void Min::run()
"linesearch alpha is zero",
"forces are zero","quadratic factors are zero"};
// compute for potential energy
int id = modify->find_compute("thermo_pe");
if (id < 0) error->all("Minimization could not find thermo_pe compute");
pe_compute = modify->compute[id];
// stats for Finish to print
ecurrent = pe_compute->compute_scalar();
@ -272,8 +322,7 @@ void Min::run()
// minimizer iterations
timer->barrier_start(TIME_LOOP);
int stop_condition = iterate(update->nsteps);
int stop_condition = iterate(nsteps);
stopstr = stopstrings[stop_condition];
// account for early exit from iterate loop due to convergence
@ -284,14 +333,17 @@ void Min::run()
// add ntimestep to all computes that store invocation times
// since are hardwireing call to thermo/dumps and computes may not be ready
if (niter < update->nsteps) {
if (niter < nsteps) {
niter++;
update->nsteps = niter;
for (int idump = 0; idump < output->ndump; idump++)
output->next_dump[idump] = update->ntimestep;
output->next_dump_any = update->ntimestep;
if (output->restart_every) output->next_restart = update->ntimestep;
if (update->restrict_output == 0) {
for (int idump = 0; idump < output->ndump; idump++)
output->next_dump[idump] = update->ntimestep;
output->next_dump_any = update->ntimestep;
if (output->restart_every == 0)
output->next_restart = update->ntimestep;
}
output->next_thermo = update->ntimestep;
modify->addstep_compute_all(update->ntimestep);
@ -299,14 +351,6 @@ void Min::run()
output->write(update->ntimestep);
}
timer->barrier_stop(TIME_LOOP);
// reset reneighboring criteria
neighbor->every = neigh_every;
neighbor->delay = neigh_delay;
neighbor->dist_check = neigh_dist_check;
// stats for Finish to print
efinal = ecurrent;
@ -314,12 +358,18 @@ void Min::run()
fnorminf_final = fnorm_inf();
}
/* ----------------------------------------------------------------------
delete fix at end of run, so its atom arrays won't persist
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void Min::cleanup()
{
// reset reneighboring criteria
neighbor->every = neigh_every;
neighbor->delay = neigh_delay;
neighbor->dist_check = neigh_dist_check;
// delete fix at end of run, so its atom arrays won't persist
modify->delete_fix("MINIMIZE");
}
@ -527,7 +577,8 @@ void Min::ev_setup()
}
/* ----------------------------------------------------------------------
set eflag,vflag for current iteration with ntimestep
set eflag,vflag for current iteration
based on computes that need info on this ntimestep
always set eflag_global = 1, since need energy every iteration
eflag = 0 = no energy computation
eflag = 1 = global energy only

3
src/min.h
View File

@ -30,7 +30,8 @@ class Min : protected Pointers {
virtual ~Min();
void init();
void setup();
void run();
void setup_minimal(int);
void run(int);
void cleanup();
void request(class Pair *, int, double);
double memory_usage() {return 0.0;}

7
src/minimize.cpp
View File

@ -17,6 +17,7 @@
#include "update.h"
#include "min.h"
#include "finish.h"
#include "timer.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -48,7 +49,11 @@ void Minimize::command(int narg, char **arg)
lmp->init();
update->minimize->setup();
update->minimize->run();
timer->barrier_start(TIME_LOOP);
update->minimize->run(update->nsteps);
timer->barrier_stop(TIME_LOOP);
update->minimize->cleanup();
Finish finish(lmp);

41
src/output.cpp
View File

@ -135,7 +135,7 @@ void Output::setup(int flag)
// if no dumps, set next_dump_any to last+1 so will not influence next
// dump custom may invoke computes so wrap with clear/add
if (ndump) {
if (ndump && update->restrict_output == 0) {
for (int idump = 0; idump < ndump; idump++) {
if (strcmp(dump[idump]->style,"custom") == 0)
modify->clearstep_compute();
@ -158,7 +158,7 @@ void Output::setup(int flag)
// will not write on last step of run unless multiple of every
// if every = 0, set next_restart to last+1 so will not influence next
if (restart_every)
if (restart_every && update->restrict_output == 0)
next_restart = (ntimestep/restart_every)*restart_every + restart_every;
else next_restart = update->laststep + 1;
@ -258,6 +258,43 @@ void Output::write(int ntimestep)
next = MYMIN(next,next_thermo);
}
/* ----------------------------------------------------------------------
force a snapshot to be written for all dumps
------------------------------------------------------------------------- */
void Output::write_dump(int ntimestep)
{
for (int idump = 0; idump < ndump; idump++) {
dump[idump]->write();
last_dump[idump] = ntimestep;
}
}
/* ----------------------------------------------------------------------
force a restart file to be written
------------------------------------------------------------------------- */
void Output::write_restart(int ntimestep)
{
if (restart_toggle == 0) {
char *file = new char[strlen(restart1) + 16];
char *ptr = strchr(restart1,'*');
*ptr = '\0';
sprintf(file,"%s%d%s",restart1,ntimestep,ptr+1);
*ptr = '*';
restart->write(file);
delete [] file;
} else if (restart_toggle == 1) {
restart->write(restart1);
restart_toggle = 2;
} else if (restart_toggle == 2) {
restart->write(restart2);
restart_toggle = 1;
}
last_restart = ntimestep;
}
/* ----------------------------------------------------------------------
add a Dump to list of Dumps
------------------------------------------------------------------------- */

2
src/output.h
View File

@ -48,6 +48,8 @@ class Output : protected Pointers {
void init();
void setup(int); // initial output before run/min
void write(int); // output for current timestep
void write_dump(int); // force output of dump snapshots
void write_restart(int); // force output of a restart file
void add_dump(int, char **); // add a Dump to Dump list
void modify_dump(int, char **); // modify a Dump

63
src/respa.cpp
View File

@ -363,10 +363,69 @@ void Respa::setup()
}
/* ----------------------------------------------------------------------
iterate for n steps
setup without output
flag = 0 = just force calculation
flag = 1 = reneighbor and force calculation
------------------------------------------------------------------------- */
void Respa::iterate(int n)
void Respa::setup_minimal(int flag)
{
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
if (flag) {
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
neighbor->build();
neighbor->ncalls = 0;
}
// compute all forces
ev_set(update->ntimestep);
for (int ilevel = 0; ilevel < nlevels; ilevel++) {
force_clear(newton[ilevel]);
if (level_bond == ilevel && force->bond)
force->bond->compute(eflag,vflag);
if (level_angle == ilevel && force->angle)
force->angle->compute(eflag,vflag);
if (level_dihedral == ilevel && force->dihedral)
force->dihedral->compute(eflag,vflag);
if (level_improper == ilevel && force->improper)
force->improper->compute(eflag,vflag);
if (level_pair == ilevel && force->pair)
force->pair->compute(eflag,vflag);
if (level_inner == ilevel && force->pair)
force->pair->compute_inner();
if (level_middle == ilevel && force->pair)
force->pair->compute_middle();
if (level_outer == ilevel && force->pair)
force->pair->compute_outer(eflag,vflag);
if (level_kspace == ilevel && force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
}
if (newton[ilevel]) comm->reverse_communicate();
copy_f_flevel(ilevel);
}
modify->setup(vflag);
sum_flevel_f();
}
/* ----------------------------------------------------------------------
run for N steps
------------------------------------------------------------------------- */
void Respa::run(int n)
{
int ntimestep;

3
src/respa.h
View File

@ -37,7 +37,8 @@ class Respa : public Integrate {
~Respa();
void init();
void setup();
void iterate(int);
void setup_minimal(int);
void run(int);
void cleanup();
void reset_dt();

4
src/run.cpp
View File

@ -148,7 +148,7 @@ void Run::command(int narg, char **arg)
}
timer->barrier_start(TIME_LOOP);
update->integrate->iterate(nsteps);
update->integrate->run(nsteps);
timer->barrier_stop(TIME_LOOP);
update->integrate->cleanup();
@ -186,7 +186,7 @@ void Run::command(int narg, char **arg)
}
timer->barrier_start(TIME_LOOP);
update->integrate->iterate(nsteps);
update->integrate->run(nsteps);
timer->barrier_stop(TIME_LOOP);
update->integrate->cleanup();

2
src/temper.cpp
View File

@ -196,7 +196,7 @@ void Temper::command(int narg, char **arg)
// run for nevery timesteps
update->integrate->iterate(nevery);
update->integrate->run(nevery);
// compute PE
// notify compute it will be called at next swap

2
src/update.cpp
View File

@ -45,6 +45,8 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp)
firststep = laststep = 0;
beginstep = endstep = 0;
restrict_output = 0;
eflag_global = vflag_global = -1;
unit_style = NULL;

3
src/update.h
View File

@ -29,8 +29,9 @@ class Update : protected Pointers {
int beginstep,endstep; // 1st and last step of multiple runs
int first_update; // 0 before initial update, 1 after
int max_eval; // max force evaluations for minimizer
int restrict_output; // 1 if output should not write dump/restart
int eflag_global,eflag_atom; // timestep global/peratom eng is tallied
int eflag_global,eflag_atom; // timestep global/peratom eng is tallied on
int vflag_global,vflag_atom; // ditto for virial
char *unit_style;

53
src/verlet.cpp
View File

@ -122,10 +122,59 @@ void Verlet::setup()
}
/* ----------------------------------------------------------------------
iterate for n steps
setup without output
flag = 0 = just force calculation
flag = 1 = reneighbor and force calculation
------------------------------------------------------------------------- */
void Verlet::iterate(int n)
void Verlet::setup_minimal(int flag)
{
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
if (flag) {
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
neighbor->build();
neighbor->ncalls = 0;
}
// compute all forces
ev_set(update->ntimestep);
force_clear();
if (force->pair) force->pair->compute(eflag,vflag);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
}
if (force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
}
if (force->newton) comm->reverse_communicate();
modify->setup(vflag);
}
/* ----------------------------------------------------------------------
run for N steps
------------------------------------------------------------------------- */
void Verlet::run(int n)
{
int nflag,ntimestep;

3
src/verlet.h
View File

@ -24,7 +24,8 @@ class Verlet : public Integrate {
~Verlet() {}
void init();
void setup();
void iterate(int);
void setup_minimal(int);
void run(int);
private:
int triclinic; // 0 if domain is orthog, 1 if triclinic