Added tad example (2b8ae7a8) · Commits · 郑智淋 / lammps

src/finish.cpp

+93 −3

Original line number	Diff line number	Diff line
		@@ -43,7 +43,7 @@ void Finish::end(int flag)
		{
		int i,m,nneigh,nneighfull;
		int histo[10];
		int loopflag,minflag,prdflag,timeflag,fftflag,histoflag,neighflag;
		int loopflag,minflag,prdflag,tadflag,timeflag,fftflag,histoflag,neighflag;
		double time,tmp,ave,max,min;
		double time_loop,time_other;
		bigint natoms;
		@@ -57,9 +57,10 @@ void Finish::end(int flag)
		// flag = 0 = just loop summary
		// flag = 1 = dynamics or minimization
		// flag = 2 = PRD
		// flag = 3 = TAD

		loopflag = 1;
		minflag = prdflag = timeflag = fftflag = histoflag = neighflag = 0;
		minflag = prdflag = tadflag = timeflag = fftflag = histoflag = neighflag = 0;

		if (flag == 1) {
		if (update->whichflag == 2) minflag = 1;
		@@ -69,6 +70,10 @@ void Finish::end(int flag)
		if (flag == 2) {
		prdflag = histoflag = neighflag = 1;

		}
		if (flag == 3) {
		tadflag = histoflag = neighflag = 1;

		}

		// loop stats
		@@ -155,7 +160,6 @@ void Finish::end(int flag)
		}
		}


		// PRD stats using PAIR,BOND,KSPACE for dephase,dynamics,quench

		if (prdflag) {
		@@ -216,6 +220,92 @@ void Finish::end(int flag)
		}
		}

		// TAD stats using PAIR,BOND,KSPACE for neb,dynamics,quench

		if (tadflag) {
		if (me == 0) {
		if (screen) fprintf(screen,"\n");
		if (logfile) fprintf(logfile,"\n");
		}

		if (screen) fprintf(screen,"TAD stats:\n");
		if (logfile) fprintf(logfile,"TAD stats:\n");

		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," NEB time (%%) = %g (%g)\n",
		time,time/time_loop*100.0);
		if (logfile)
		fprintf(logfile," NEB time (%%) = %g (%g)\n",
		time,time/time_loop*100.0);
		}

		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," Dynamics time (%%) = %g (%g)\n",
		time,time/time_loop*100.0);
		if (logfile)
		fprintf(logfile," Dynamics time (%%) = %g (%g)\n",
		time,time/time_loop*100.0);
		}

		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," Quench time (%%) = %g (%g)\n",
		time,time/time_loop*100.0);
		if (logfile)
		fprintf(logfile," Quench 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," Output time (%%) = %g (%g)\n",
		time,time/time_loop*100.0);
		if (logfile)
		fprintf(logfile," Output 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);
		}
		}

		// timing breakdowns

		if (timeflag) {

src/min_fire.cpp

+33 −0

Original line number	Diff line number	Diff line
		@@ -106,6 +106,14 @@ int MinFire::iterate(int maxiter)
		vdotf += v[i][0]f[i][0] + v[i][1]f[i][1] + v[i][2]*f[i][2];
		MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,world);

		// sum vdotf over replicas, if necessary
		// this communicator would be invalid for multiprocess replicas

		if (update->multireplica == 1) {
		vdotf = vdotfall;
		MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
		}

		// if (v dot f) > 0:
		// v = (1-alpha) v + alpha \|v\| Fhat
		// \|v\| = length of v, Fhat = unit f
		@@ -117,11 +125,28 @@ int MinFire::iterate(int maxiter)
		for (int i = 0; i < nlocal; i++)
		vdotv += v[i][0]v[i][0] + v[i][1]v[i][1] + v[i][2]*v[i][2];
		MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,world);

		// sum vdotv over replicas, if necessary
		// this communicator would be invalid for multiprocess replicas

		if (update->multireplica == 1) {
		vdotv = vdotvall;
		MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
		}

		fdotf = 0.0;
		for (int i = 0; i < nlocal; i++)
		fdotf += f[i][0]f[i][0] + f[i][1]f[i][1] + f[i][2]*f[i][2];
		MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,world);

		// sum fdotf over replicas, if necessary
		// this communicator would be invalid for multiprocess replicas

		if (update->multireplica == 1) {
		fdotf = fdotfall;
		MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
		}

		scale1 = 1.0 - alpha;
		if (fdotfall == 0.0) scale2 = 0.0;
		else scale2 = alpha * sqrt(vdotvall/fdotfall);
		@@ -162,6 +187,14 @@ int MinFire::iterate(int maxiter)
		}
		MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,world);

		// min dtv over replicas, if necessary
		// this communicator would be invalid for multiprocess replicas

		if (update->multireplica == 1) {
		dtvone = dtv;
		MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,universe->uworld);
		}

		// Euler integration step

		double **x = atom->x;

src/min_quickmin.cpp

+25 −0

Original line number	Diff line number	Diff line
		@@ -102,6 +102,14 @@ int MinQuickMin::iterate(int maxiter)
		vdotf += v[i][0]f[i][0] + v[i][1]f[i][1] + v[i][2]*f[i][2];
		MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,world);

		// sum vdotf over replicas, if necessary
		// this communicator would be invalid for multiprocess replicas

		if (update->multireplica == 1) {
		vdotf = vdotfall;
		MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
		}

		if (vdotfall < 0.0) {
		last_negative = ntimestep;
		for (int i = 0; i < nlocal; i++)
		@@ -112,6 +120,15 @@ int MinQuickMin::iterate(int maxiter)
		for (int i = 0; i < nlocal; i++)
		fdotf += f[i][0]f[i][0] + f[i][1]f[i][1] + f[i][2]*f[i][2];
		MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,world);

		// sum fdotf over replicas, if necessary
		// this communicator would be invalid for multiprocess replicas

		if (update->multireplica == 1) {
		fdotf = fdotfall;
		MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
		}

		if (fdotfall == 0.0) scale = 0.0;
		else scale = vdotfall/fdotfall;
		for (int i = 0; i < nlocal; i++) {
		@@ -136,6 +153,14 @@ int MinQuickMin::iterate(int maxiter)
		}
		MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,world);

		// min dtv over replicas, if necessary
		// this communicator would be invalid for multiprocess replicas

		if (update->multireplica == 1) {
		dtvone = dtv;
		MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,universe->uworld);
		}

		// Euler integration step

		double **x = atom->x;

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