more formatting cleanup (9008a311) · Commits · 郑智淋 / lammps

src/REPLICA/neb.cpp

+102 −81

Original line number	Diff line number	Diff line
		@@ -156,8 +156,8 @@ void NEB::command(int narg, char **arg)
		if (narg != 6 && narg !=7) error->universe_all(FLERR,"Illegal NEB command");
		} else error->universe_all(FLERR,"Illegal NEB command");

		Verbose=false;
		if (strcmp(arg[narg-1],"verbose") == 0) Verbose=true;
		verbose=false;
		if (strcmp(arg[narg-1],"verbose") == 0) verbose=true;
		// run the NEB calculation

		run();
		@@ -182,7 +182,7 @@ void NEB::run()
		if (ineb == modify->nfix) error->all(FLERR,"NEB requires use of fix neb");

		fneb = (FixNEB *) modify->fix[ineb];
		if (Verbose) numall =7;
		if (verbose) numall =7;
		else numall = 4;
		memory->create(all,nreplica,numall,"neb:all");
		rdist = new double[nreplica];
		@@ -200,9 +200,11 @@ void NEB::run()
		error->all(FLERR,"NEB requires damped dynamics minimizer");

		// setup regular NEB minimization
		FILE *uscreen = universe->uscreen;
		FILE *ulogfile = universe->ulogfile;

		if (me_universe == 0 && universe->uscreen)
		fprintf(universe->uscreen,"Setting up regular NEB ...\n");
		if (me_universe == 0 && uscreen)
		fprintf(uscreen,"Setting up regular NEB ...\n");

		update->beginstep = update->firststep = update->ntimestep;
		update->endstep = update->laststep = update->firststep + n1steps;
		@@ -214,29 +216,29 @@ void NEB::run()
		update->minimize->setup();

		if (me_universe == 0) {
		if (universe->uscreen) {
		if (Verbose) {
		fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
		if (uscreen) {
		if (verbose) {
		fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce "
		"GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
		"RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 "
		"ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 "
		"... ReplicaForceN MaxAtomForceN\n");
		} else {
		fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
		fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce "
		"GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
		"RDN PEN\n");
		}
		}

		if (universe->ulogfile) {
		if (Verbose) {
		fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
		if (ulogfile) {
		if (verbose) {
		fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce "
		"GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
		"RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 "
		"ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 "
		"... ReplicaForceN MaxAtomForceN\n");
		} else {
		fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
		fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce "
		"GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
		"RDN PEN\n");
		}
		@@ -279,14 +281,14 @@ void NEB::run()
		// setup climbing NEB minimization
		// must reinitialize minimizer so it re-creates its fix MINIMIZE

		if (me_universe == 0 && universe->uscreen)
		fprintf(universe->uscreen,"Setting up climbing ...\n");
		if (me_universe == 0 && uscreen)
		fprintf(uscreen,"Setting up climbing ...\n");

		if (me_universe == 0) {
		if (universe->uscreen)
		fprintf(universe->uscreen,"Climbing replica = %d\n",top+1);
		if (universe->ulogfile)
		fprintf(universe->ulogfile,"Climbing replica = %d\n",top+1);
		if (uscreen)
		fprintf(uscreen,"Climbing replica = %d\n",top+1);
		if (ulogfile)
		fprintf(ulogfile,"Climbing replica = %d\n",top+1);
		}

		update->beginstep = update->firststep = update->ntimestep;
		@@ -301,30 +303,35 @@ void NEB::run()
		update->minimize->setup();

		if (me_universe == 0) {
		if (universe->uscreen)
		if (Verbose)
		fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
		"GradV0 GradV1 GradVc "
		"EBF EBR RDT "
		"RD1 PE1 RD2 PE2 ... RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 ... ReplicaForceN MaxAtomForceN\n");
		else
		fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
		if (uscreen)
		if (verbose) {
		fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce "
		"GradV0 GradV1 GradVc EBF EBR RDT "
		"RD1 PE1 RD2 PE2 ... RDN PEN "
		"pathangle1 angletangrad1 anglegrad1 gradV1 "
		"ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 "
		"... ReplicaForceN MaxAtomForceN\n");
		} else {
		fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce "
		"GradV0 GradV1 GradVc "
		"EBF EBR RDT "
		"RD1 PE1 RD2 PE2 ... RDN PEN\n");
		if (universe->ulogfile)
		if (Verbose)
		fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
		"GradV0 GradV1 GradVc "
		"EBF EBR RDT "
		"RD1 PE1 RD2 PE2 ... RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 ... ReplicaForceN MaxAtomForceN\n");
		else

		fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
		}
		if (ulogfile)
		if (verbose) {
		fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce "
		"GradV0 GradV1 GradVc EBF EBR RDT "
		"RD1 PE1 RD2 PE2 ... RDN PEN "
		"pathangle1 angletangrad1 anglegrad1 gradV1 "
		"ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 "
		"... ReplicaForceN MaxAtomForceN\n");
		} else {
		fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce "
		"GradV0 GradV1 GradVc "
		"EBF EBR RDT "
		"RD1 PE1 RD2 PE2 ... RDN PEN\n");
		}
		}
		print_status();

		// perform climbing NEB for n2steps or until replicas converge
		@@ -574,8 +581,7 @@ void NEB::print_status()
		double fmaxatom;
		MPI_Allreduce(&fnorminf,&fmaxatom,1,MPI_DOUBLE,MPI_MAX,roots);

		if (Verbose)
		{
		if (verbose) {
		freplica = new double[nreplica];
		MPI_Allgather(&fnorm2,1,MPI_DOUBLE,&freplica[0],1,MPI_DOUBLE,roots);
		fmaxatomInRepl = new double[nreplica];
		@@ -588,12 +594,10 @@ void NEB::print_status()
		one[2] = fneb->nlen;
		one[3] = fneb->gradlen;

		if (Verbose)
		{
		if (verbose) {
		one[4] = fneb->dotpath;
		one[5] = fneb->dottangrad;
		one[6] = fneb->dotgrad;

		}

		if (output->thermo->normflag) one[0] /= atom->natoms;
		@@ -639,39 +643,56 @@ void NEB::print_status()
		}

		if (me_universe == 0) {
		if (universe->uscreen) {
		fprintf(universe->uscreen,BIGINT_FORMAT " %12.8g %12.8g ",
		const double todeg=180.0/MY_PI;
		FILE *uscreen = universe->uscreen;
		FILE *ulogfile = universe->ulogfile;
		if (uscreen) {
		fprintf(uscreen,BIGINT_FORMAT " %12.8g %12.8g ",
		update->ntimestep,fmaxreplica,fmaxatom);
		fprintf(universe->uscreen,"%12.8g %12.8g %12.8g ",
		fprintf(uscreen,"%12.8g %12.8g %12.8g ",
		gradvnorm0,gradvnorm1,gradvnormc);
		fprintf(universe->uscreen,"%12.8g %12.8g %12.8g ",ebf,ebr,endpt);
		fprintf(uscreen,"%12.8g %12.8g %12.8g ",ebf,ebr,endpt);
		for (int i = 0; i < nreplica; i++)
		fprintf(universe->uscreen,"%12.8g %12.8g ",rdist[i],all[i][0]);
		if (Verbose)
		{fprintf(universe->uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",NAN,180-acos(all[0][5])180/MY_PI,180-acos(all[0][6])180/MY_PI,all[0][3],freplica[0],fmaxatomInRepl[0]);
		fprintf(uscreen,"%12.8g %12.8g ",rdist[i],all[i][0]);
		if (verbose) {
		fprintf(uscreen,"NaN %12.5g %12.5g %12.5g %12.5g %12.5g",
		180-acos(all[0][5])todeg,180-acos(all[0][6])todeg,
		all[0][3],freplica[0],fmaxatomInRepl[0]);
		for (int i = 1; i < nreplica-1; i++)
		fprintf(universe->uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",180-acos(all[i][4])180/MY_PI,180-acos(all[i][5])180/MY_PI,180-acos(all[i][6])*180/MY_PI,all[i][3],freplica[i],fmaxatomInRepl[i]);
		fprintf(universe->uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",NAN,180-acos(all[nreplica-1][5])*180/MY_PI,NAN,all[nreplica-1][3],freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
		fprintf(uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
		180-acos(all[i][4])todeg,180-acos(all[i][5])todeg,
		180-acos(all[i][6])*todeg,all[i][3],freplica[i],
		fmaxatomInRepl[i]);
		fprintf(uscreen,"NaN %12.5g NaN %12.5g %12.5g %12.5g",
		180-acos(all[nreplica-1][5])*todeg,all[nreplica-1][3],
		freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
		}
		fprintf(universe->uscreen,"\n");
		fprintf(uscreen,"\n");
		}

		if (universe->ulogfile) {
		fprintf(universe->ulogfile,BIGINT_FORMAT " %12.8g %12.8g ",
		if (ulogfile) {
		fprintf(ulogfile,BIGINT_FORMAT " %12.8g %12.8g ",
		update->ntimestep,fmaxreplica,fmaxatom);
		fprintf(universe->ulogfile,"%12.8g %12.8g %12.8g ",
		fprintf(ulogfile,"%12.8g %12.8g %12.8g ",
		gradvnorm0,gradvnorm1,gradvnormc);
		fprintf(universe->ulogfile,"%12.8g %12.8g %12.8g ",ebf,ebr,endpt);
		fprintf(ulogfile,"%12.8g %12.8g %12.8g ",ebf,ebr,endpt);
		for (int i = 0; i < nreplica; i++)
		fprintf(universe->ulogfile,"%12.8g %12.8g ",rdist[i],all[i][0]);
		if (Verbose)
		{fprintf(universe->ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",NAN,180-acos(all[0][5])180/MY_PI,180-acos(all[0][6])180/MY_PI,all[0][3],freplica[0],fmaxatomInRepl[0]);
		fprintf(ulogfile,"%12.8g %12.8g ",rdist[i],all[i][0]);
		if (verbose) {
		fprintf(ulogfile,"NaN %12.5g %12.5g %12.5g %12.5g %12.5g",
		180-acos(all[0][5])todeg,180-acos(all[0][6])todeg,
		all[0][3],freplica[0],fmaxatomInRepl[0]);
		for (int i = 1; i < nreplica-1; i++)
		fprintf(universe->ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",180-acos(all[i][4])180/MY_PI,180-acos(all[i][5])180/MY_PI,180-acos(all[i][6])*180/MY_PI,all[i][3],freplica[i],fmaxatomInRepl[i]);
		fprintf(universe->ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",NAN,180-acos(all[nreplica-1][5])*180/MY_PI,NAN,all[nreplica-1][3],freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
		}
		fprintf(universe->ulogfile,"\n");
		fflush(universe->ulogfile);
		fprintf(ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
		180-acos(all[i][4])todeg,180-acos(all[i][5])todeg,
		180-acos(all[i][6])*todeg,all[i][3],freplica[i],
		fmaxatomInRepl[i]);
		fprintf(ulogfile,"NaN %12.5g NaN %12.5g %12.5g %12.5g",
		180-acos(all[nreplica-1][5])*todeg,all[nreplica-1][3],
		freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
		}
		fprintf(ulogfile,"\n");
		fflush(ulogfile);
		}
		}
		}

src/REPLICA/neb.h

+2 −2

Original line number	Diff line number	Diff line
		@@ -38,7 +38,7 @@ class NEB : protected Pointers {
		private:
		int me,me_universe; // my proc ID in world and universe
		int ireplica,nreplica;
		bool Verbose;
		bool verbose;
		MPI_Comm uworld;
		MPI_Comm roots; // MPI comm with 1 root proc from each world
		FILE *fp;
		@@ -109,7 +109,7 @@ for NEB.

		E: Too many timesteps

		The cummulative timesteps must fit in a 64-bit integer.
		The cumulative timesteps must fit in a 64-bit integer.

		E: Unexpected end of neb file

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