pair TIP4P bug fix for cutoffs >> box size (f6a81958) · Commits · 郑智淋 / lammps

src/KOKKOS/modify_kokkos.cpp

+66 −4

Original line number	Diff line number	Diff line
		@@ -81,7 +81,7 @@ void ModifyKokkos::setup_pre_exchange()
		atomKK->sync(fix[list_min_pre_exchange[i]]->execution_space,
		fix[list_min_pre_exchange[i]]->datamask_read);
		if (!fix[list_min_pre_exchange[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
		fix[list_min_pre_exchange[i]]->min_setup_pre_exchange();
		fix[list_min_pre_exchange[i]]->setup_pre_exchange();
		lmp->kokkos->auto_sync = 0;
		atomKK->modified(fix[list_min_pre_exchange[i]]->execution_space,
		fix[list_min_pre_exchange[i]]->datamask_modify);
		@@ -110,7 +110,7 @@ void ModifyKokkos::setup_pre_neighbor()
		atomKK->sync(fix[list_min_pre_neighbor[i]]->execution_space,
		fix[list_min_pre_neighbor[i]]->datamask_read);
		if (!fix[list_min_pre_neighbor[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
		fix[list_min_pre_neighbor[i]]->min_setup_pre_neighbor();
		fix[list_min_pre_neighbor[i]]->setup_pre_neighbor();
		lmp->kokkos->auto_sync = 0;
		atomKK->modified(fix[list_min_pre_neighbor[i]]->execution_space,
		fix[list_min_pre_neighbor[i]]->datamask_modify);
		@@ -139,13 +139,42 @@ void ModifyKokkos::setup_pre_force(int vflag)
		atomKK->sync(fix[list_min_pre_force[i]]->execution_space,
		fix[list_min_pre_force[i]]->datamask_read);
		if (!fix[list_min_pre_force[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
		fix[list_min_pre_force[i]]->min_setup_pre_force(vflag);
		fix[list_min_pre_force[i]]->setup_pre_force(vflag);
		lmp->kokkos->auto_sync = 0;
		atomKK->modified(fix[list_min_pre_force[i]]->execution_space,
		fix[list_min_pre_force[i]]->datamask_modify);
		}
		}

		/* ----------------------------------------------------------------------
		setup pre_reverse call, only for fixes that define pre_reverse
		called from Verlet, RESPA, Min
		------------------------------------------------------------------------- */

		void ModifyKokkos::setup_pre_reverse(int eflag, int vflag)
		{
		if (update->whichflag == 1)
		for (int i = 0; i < n_pre_reverse; i++) {
		atomKK->sync(fix[list_pre_reverse[i]]->execution_space,
		fix[list_pre_reverse[i]]->datamask_read);
		if (!fix[list_pre_reverse[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
		fix[list_pre_reverse[i]]->setup_pre_reverse(eflag,vflag);
		lmp->kokkos->auto_sync = 0;
		atomKK->modified(fix[list_pre_reverse[i]]->execution_space,
		fix[list_pre_reverse[i]]->datamask_modify);
		}
		else if (update->whichflag == 2)
		for (int i = 0; i < n_min_pre_reverse; i++) {
		atomKK->sync(fix[list_min_pre_reverse[i]]->execution_space,
		fix[list_min_pre_reverse[i]]->datamask_read);
		if (!fix[list_min_pre_reverse[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
		fix[list_min_pre_reverse[i]]->setup_pre_reverse(eflag,vflag);
		lmp->kokkos->auto_sync = 0;
		atomKK->modified(fix[list_min_pre_reverse[i]]->execution_space,
		fix[list_min_pre_reverse[i]]->datamask_modify);
		}
		}

		/* ----------------------------------------------------------------------
		1st half of integrate call, only for relevant fixes
		------------------------------------------------------------------------- */
		@@ -231,6 +260,23 @@ void ModifyKokkos::pre_force(int vflag)
		}
		}

		/* ----------------------------------------------------------------------
		pre_reverse call, only for relevant fixes
		------------------------------------------------------------------------- */

		void ModifyKokkos::pre_reverse(int eflag, int vflag)
		{
		for (int i = 0; i < n_pre_reverse; i++) {
		atomKK->sync(fix[list_pre_reverse[i]]->execution_space,
		fix[list_pre_reverse[i]]->datamask_read);
		if (!fix[list_pre_reverse[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
		fix[list_pre_reverse[i]]->pre_reverse(eflag,vflag);
		lmp->kokkos->auto_sync = 0;
		atomKK->modified(fix[list_pre_reverse[i]]->execution_space,
		fix[list_pre_reverse[i]]->datamask_modify);
		}
		}

		/* ----------------------------------------------------------------------
		post_force call, only for relevant fixes
		------------------------------------------------------------------------- */
		@@ -476,6 +522,23 @@ void ModifyKokkos::min_pre_force(int vflag)
		}
		}

		/* ----------------------------------------------------------------------
		minimizer pre-reverse call, only for relevant fixes
		------------------------------------------------------------------------- */

		void ModifyKokkos::min_pre_reverse(int eflag, int vflag)
		{
		for (int i = 0; i < n_min_pre_reverse; i++) {
		atomKK->sync(fix[list_min_pre_reverse[i]]->execution_space,
		fix[list_min_pre_reverse[i]]->datamask_read);
		if (!fix[list_min_pre_reverse[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
		fix[list_min_pre_reverse[i]]->min_pre_reverse(eflag,vflag);
		lmp->kokkos->auto_sync = 0;
		atomKK->modified(fix[list_min_pre_reverse[i]]->execution_space,
		fix[list_min_pre_reverse[i]]->datamask_modify);
		}
		}

		/* ----------------------------------------------------------------------
		minimizer force adjustment call, only for relevant fixes
		------------------------------------------------------------------------- */
		@@ -658,4 +721,3 @@ int ModifyKokkos::min_reset_ref()
		}
		return itmpall;
		}

src/KOKKOS/modify_kokkos.h

+3 −0

Original line number	Diff line number	Diff line
		@@ -26,12 +26,14 @@ class ModifyKokkos : public Modify {
		void setup_pre_exchange();
		void setup_pre_neighbor();
		void setup_pre_force(int);
		void setup_pre_reverse(int, int);
		void initial_integrate(int);
		void post_integrate();
		void pre_decide();
		void pre_exchange();
		void pre_neighbor();
		void pre_force(int);
		void pre_reverse(int,int);
		void post_force(int);
		void final_integrate();
		void end_of_step();
		@@ -48,6 +50,7 @@ class ModifyKokkos : public Modify {
		void min_pre_exchange();
		void min_pre_neighbor();
		void min_pre_force(int);
		void min_pre_reverse(int,int);
		void min_post_force(int);

		double min_energy(double *);

src/KSPACE/pair_lj_cut_tip4p_long.cpp

+24 −16

Original line number	Diff line number	Diff line
		@@ -88,8 +88,8 @@ void PairLJCutTIP4PLong::compute(int eflag, int vflag)
		double r,r2inv,r6inv,forcecoul,forcelj,cforce;
		double factor_coul,factor_lj;
		double grij,expm2,prefactor,t,erfc;
		double fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];
		double x1,x2;
		double fO[3],fH[3],fd[3],v[6];
		double x1,x2,xH1,xH2;
		int ilist,jlist,numneigh,*firstneigh;
		double rsq;

		@@ -146,14 +146,20 @@ void PairLJCutTIP4PLong::compute(int eflag, int vflag)

		if (itype == typeO) {
		if (hneigh[i][0] < 0) {
		hneigh[i][0] = iH1 = atom->map(tag[i] + 1);
		hneigh[i][1] = iH2 = atom->map(tag[i] + 2);
		hneigh[i][2] = 1;
		iH1 = atom->map(tag[i] + 1);
		iH2 = atom->map(tag[i] + 2);
		if (iH1 == -1 \|\| iH2 == -1)
		error->one(FLERR,"TIP4P hydrogen is missing");
		if (atom->type[iH1] != typeH \|\| atom->type[iH2] != typeH)
		error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
		// set iH1,iH2 to closest image to O
		iH1 = domain->closest_image(i,iH1);
		iH2 = domain->closest_image(i,iH2);
		compute_newsite(x[i],x[iH1],x[iH2],newsite[i]);
		hneigh[i][0] = iH1;
		hneigh[i][1] = iH2;
		hneigh[i][2] = 1;

		} else {
		iH1 = hneigh[i][0];
		iH2 = hneigh[i][1];
		@@ -216,14 +222,20 @@ void PairLJCutTIP4PLong::compute(int eflag, int vflag)

		if (jtype == typeO) {
		if (hneigh[j][0] < 0) {
		hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
		hneigh[j][1] = jH2 = atom->map(tag[j] + 2);
		hneigh[j][2] = 1;
		jH1 = atom->map(tag[j] + 1);
		jH2 = atom->map(tag[j] + 2);
		if (jH1 == -1 \|\| jH2 == -1)
		error->one(FLERR,"TIP4P hydrogen is missing");
		if (atom->type[jH1] != typeH \|\| atom->type[jH2] != typeH)
		error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
		// set jH1,jH2 to closest image to O
		jH1 = domain->closest_image(j,jH1);
		jH2 = domain->closest_image(j,jH2);
		compute_newsite(x[j],x[jH1],x[jH2],newsite[j]);
		hneigh[j][0] = jH1;
		hneigh[j][1] = jH2;
		hneigh[j][2] = 1;

		} else {
		jH1 = hneigh[j][0];
		jH2 = hneigh[j][1];
		@@ -327,9 +339,8 @@ void PairLJCutTIP4PLong::compute(int eflag, int vflag)
		f[iH2][2] += fH[2];

		if (vflag) {
		domain->closest_image(x[i],x[iH1],xH1);
		domain->closest_image(x[i],x[iH2],xH2);

		xH1 = x[iH1];
		xH2 = x[iH2];
		v[0] = x[i][0]fO[0] + xH1[0]fH[0] + xH2[0]*fH[0];
		v[1] = x[i][1]fO[1] + xH1[1]fH[1] + xH2[1]*fH[1];
		v[2] = x[i][2]fO[2] + xH1[2]fH[2] + xH2[2]*fH[2];
		@@ -385,9 +396,8 @@ void PairLJCutTIP4PLong::compute(int eflag, int vflag)
		f[jH2][2] += fH[2];

		if (vflag) {
		domain->closest_image(x[j],x[jH1],xH1);
		domain->closest_image(x[j],x[jH2],xH2);

		xH1 = x[jH1];
		xH2 = x[jH2];
		v[0] += x[j][0]fO[0] + xH1[0]fH[0] + xH2[0]*fH[0];
		v[1] += x[j][1]fO[1] + xH1[1]fH[1] + xH2[1]*fH[1];
		v[2] += x[j][2]fO[2] + xH1[2]fH[2] + xH2[2]*fH[2];
		@@ -565,12 +575,10 @@ void PairLJCutTIP4PLong::compute_newsite(double xO, double xH1,
		double delx1 = xH1[0] - xO[0];
		double dely1 = xH1[1] - xO[1];
		double delz1 = xH1[2] - xO[2];
		domain->minimum_image(delx1,dely1,delz1);

		double delx2 = xH2[0] - xO[0];
		double dely2 = xH2[1] - xO[1];
		double delz2 = xH2[2] - xO[2];
		domain->minimum_image(delx2,dely2,delz2);

		xM[0] = xO[0] + alpha * 0.5 * (delx1 + delx2);
		xM[1] = xO[1] + alpha * 0.5 * (dely1 + dely2);

src/KSPACE/pair_lj_long_tip4p_long.cpp

+24 −16

Original line number	Diff line number	Diff line
		@@ -86,8 +86,8 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
		double r,r2inv,forcecoul,forcelj,cforce;
		double factor_coul;
		double grij,expm2,prefactor,t,erfc;
		double fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];// f1[3];
		double x1,x2;
		double fO[3],fH[3],fd[3],v[6];
		double x1,x2,xH1,xH2;
		int ilist,jlist,numneigh,*firstneigh;
		double rsq;

		@@ -145,14 +145,20 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
		itype = type[i];
		if (itype == typeO) {
		if (hneigh[i][0] < 0) {
		hneigh[i][0] = iH1 = atom->map(tag[i] + 1);
		hneigh[i][1] = iH2 = atom->map(tag[i] + 2);
		hneigh[i][2] = 1;
		iH1 = atom->map(tag[i] + 1);
		iH2 = atom->map(tag[i] + 2);
		if (iH1 == -1 \|\| iH2 == -1)
		error->one(FLERR,"TIP4P hydrogen is missing");
		if (atom->type[iH1] != typeH \|\| atom->type[iH2] != typeH)
		error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
		// set iH1,iH2 to closest image to O
		iH1 = domain->closest_image(i,iH1);
		iH2 = domain->closest_image(i,iH2);
		compute_newsite(x[i],x[iH1],x[iH2],newsite[i]);
		hneigh[i][0] = iH1;
		hneigh[i][1] = iH2;
		hneigh[i][2] = 1;

		} else {
		iH1 = hneigh[i][0];
		iH2 = hneigh[i][1];
		@@ -253,14 +259,20 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
		if (itype == typeO \|\| jtype == typeO) {
		if (jtype == typeO) {
		if (hneigh[j][0] < 0) {
		hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
		hneigh[j][1] = jH2 = atom->map(tag[j] + 2);
		hneigh[j][2] = 1;
		jH1 = atom->map(tag[j] + 1);
		jH2 = atom->map(tag[j] + 2);
		if (jH1 == -1 \|\| jH2 == -1)
		error->one(FLERR,"TIP4P hydrogen is missing");
		if (atom->type[jH1] != typeH \|\| atom->type[jH2] != typeH)
		error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
		// set jH1,jH2 to closest image to O
		jH1 = domain->closest_image(j,jH1);
		jH2 = domain->closest_image(j,jH2);
		compute_newsite(x[j],x[jH1],x[jH2],newsite[j]);
		hneigh[j][0] = jH1;
		hneigh[j][1] = jH2;
		hneigh[j][2] = 1;

		} else {
		jH1 = hneigh[j][0];
		jH2 = hneigh[j][1];
		@@ -365,9 +377,8 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
		f[iH2][2] += fH[2];

		if (vflag) {
		domain->closest_image(x[i],x[iH1],xH1);
		domain->closest_image(x[i],x[iH2],xH2);

		xH1 = x[iH1];
		xH2 = x[iH2];
		v[0] = x[i][0]fO[0] + xH1[0]fH[0] + xH2[0]*fH[0];
		v[1] = x[i][1]fO[1] + xH1[1]fH[1] + xH2[1]*fH[1];
		v[2] = x[i][2]fO[2] + xH1[2]fH[2] + xH2[2]*fH[2];
		@@ -423,9 +434,8 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
		f[jH2][2] += fH[2];

		if (vflag) {
		domain->closest_image(x[j],x[jH1],xH1);
		domain->closest_image(x[j],x[jH2],xH2);

		xH1 = x[jH1];
		xH2 = x[jH2];
		v[0] += x[j][0]fO[0] + xH1[0]fH[0] + xH2[0]*fH[0];
		v[1] += x[j][1]fO[1] + xH1[1]fH[1] + xH2[1]*fH[1];
		v[2] += x[j][2]fO[2] + xH1[2]fH[2] + xH2[2]*fH[2];
		@@ -1548,12 +1558,10 @@ void PairLJLongTIP4PLong::compute_newsite(double xO, double xH1,
		double delx1 = xH1[0] - xO[0];
		double dely1 = xH1[1] - xO[1];
		double delz1 = xH1[2] - xO[2];
		domain->minimum_image(delx1,dely1,delz1);

		double delx2 = xH2[0] - xO[0];
		double dely2 = xH2[1] - xO[1];
		double delz2 = xH2[2] - xO[2];
		domain->minimum_image(delx2,dely2,delz2);

		xM[0] = xO[0] + alpha * 0.5 * (delx1 + delx2);
		xM[1] = xO[1] + alpha * 0.5 * (dely1 + dely2);

src/KSPACE/pair_tip4p_long.cpp

+24 −16

Original line number	Diff line number	Diff line
		@@ -84,8 +84,8 @@ void PairTIP4PLong::compute(int eflag, int vflag)
		double r,r2inv,forcecoul,cforce;
		double factor_coul;
		double grij,expm2,prefactor,t,erfc;
		double fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];
		double x1,x2;
		double fO[3],fH[3],fd[3],v[6];
		double x1,x2,xH1,xH2;
		int ilist,jlist,numneigh,*firstneigh;
		double rsq;

		@@ -140,14 +140,20 @@ void PairTIP4PLong::compute(int eflag, int vflag)

		if (itype == typeO) {
		if (hneigh[i][0] < 0) {
		hneigh[i][0] = iH1 = atom->map(tag[i] + 1);
		hneigh[i][1] = iH2 = atom->map(tag[i] + 2);
		hneigh[i][2] = 1;
		iH1 = atom->map(tag[i] + 1);
		iH2 = atom->map(tag[i] + 2);
		if (iH1 == -1 \|\| iH2 == -1)
		error->one(FLERR,"TIP4P hydrogen is missing");
		if (atom->type[iH1] != typeH \|\| atom->type[iH2] != typeH)
		error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
		// set iH1,iH2 to closest image to O
		iH1 = domain->closest_image(i,iH1);
		iH2 = domain->closest_image(i,iH2);
		compute_newsite(x[i],x[iH1],x[iH2],newsite[i]);
		hneigh[i][0] = iH1;
		hneigh[i][1] = iH2;
		hneigh[i][2] = 1;

		} else {
		iH1 = hneigh[i][0];
		iH2 = hneigh[i][1];
		@@ -184,14 +190,20 @@ void PairTIP4PLong::compute(int eflag, int vflag)

		if (jtype == typeO) {
		if (hneigh[j][0] < 0) {
		hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
		hneigh[j][1] = jH2 = atom->map(tag[j] + 2);
		hneigh[j][2] = 1;
		jH1 = atom->map(tag[j] + 1);
		jH2 = atom->map(tag[j] + 2);
		if (jH1 == -1 \|\| jH2 == -1)
		error->one(FLERR,"TIP4P hydrogen is missing");
		if (atom->type[jH1] != typeH \|\| atom->type[jH2] != typeH)
		error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
		// set jH1,jH2 to closest image to O
		jH1 = domain->closest_image(j,jH1);
		jH2 = domain->closest_image(j,jH2);
		compute_newsite(x[j],x[jH1],x[jH2],newsite[j]);
		hneigh[j][0] = jH1;
		hneigh[j][1] = jH2;
		hneigh[j][2] = 1;

		} else {
		jH1 = hneigh[j][0];
		jH2 = hneigh[j][1];
		@@ -295,9 +307,8 @@ void PairTIP4PLong::compute(int eflag, int vflag)
		f[iH2][2] += fH[2];

		if (vflag) {
		domain->closest_image(x[i],x[iH1],xH1);
		domain->closest_image(x[i],x[iH2],xH2);

		xH1 = x[iH1];
		xH2 = x[iH2];
		v[0] = x[i][0]fO[0] + xH1[0]fH[0] + xH2[0]*fH[0];
		v[1] = x[i][1]fO[1] + xH1[1]fH[1] + xH2[1]*fH[1];
		v[2] = x[i][2]fO[2] + xH1[2]fH[2] + xH2[2]*fH[2];
		@@ -353,9 +364,8 @@ void PairTIP4PLong::compute(int eflag, int vflag)
		f[jH2][2] += fH[2];

		if (vflag) {
		domain->closest_image(x[j],x[jH1],xH1);
		domain->closest_image(x[j],x[jH2],xH2);

		xH1 = x[jH1];
		xH2 = x[jH2];
		v[0] += x[j][0]fO[0] + xH1[0]fH[0] + xH2[0]*fH[0];
		v[1] += x[j][1]fO[1] + xH1[1]fH[1] + xH2[1]*fH[1];
		v[2] += x[j][2]fO[2] + xH1[2]fH[2] + xH2[2]*fH[2];
		@@ -488,12 +498,10 @@ void PairTIP4PLong::compute_newsite(double xO, double xH1,
		double delx1 = xH1[0] - xO[0];
		double dely1 = xH1[1] - xO[1];
		double delz1 = xH1[2] - xO[2];
		domain->minimum_image(delx1,dely1,delz1);

		double delx2 = xH2[0] - xO[0];
		double dely2 = xH2[1] - xO[1];
		double delz2 = xH2[2] - xO[2];
		domain->minimum_image(delx2,dely2,delz2);

		xM[0] = xO[0] + alpha * 0.5 * (delx1 + delx2);
		xM[1] = xO[1] + alpha * 0.5 * (dely1 + dely2);

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