(3333f6a9) · Commits · 郑智淋 / lammps

src/atom.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -32,8 +32,8 @@ class Atom : protected Pointers {
		int tag_enable; // 0/1 if atom ID tags are defined
		int molecular; // 0 = atomic, 1 = molecular system

		bigint nbonds,nangles,ndihedrals,nimpropers;
		int ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
		int nbonds,nangles,ndihedrals,nimpropers;
		int bond_per_atom,angle_per_atom,dihedral_per_atom,improper_per_atom;
		int extra_bond_per_atom;

src/delete_bonds.cpp

+33 −29

Original line number	Diff line number	Diff line
		@@ -339,30 +339,32 @@ void DeleteBonds::command(int narg, char **arg)
		if (remove_flag) {

		if (atom->avec->bonds_allow) {
		int nbonds = 0;
		bigint nbonds = 0;
		for (i = 0; i < nlocal; i++) nbonds += atom->num_bond[i];
		MPI_Allreduce(&nbonds,&atom->nbonds,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&nbonds,&atom->nbonds,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
		if (force->newton_bond == 0) atom->nbonds /= 2;
		}

		if (atom->avec->angles_allow) {
		int nangles = 0;
		bigint nangles = 0;
		for (i = 0; i < nlocal; i++) nangles += atom->num_angle[i];
		MPI_Allreduce(&nangles,&atom->nangles,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&nangles,&atom->nangles,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
		if (force->newton_bond == 0) atom->nangles /= 3;
		}

		if (atom->avec->dihedrals_allow) {
		int ndihedrals = 0;
		bigint ndihedrals = 0;
		for (i = 0; i < nlocal; i++) ndihedrals += atom->num_dihedral[i];
		MPI_Allreduce(&ndihedrals,&atom->ndihedrals,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&ndihedrals,&atom->ndihedrals,
		1,MPI_UNSIGNED_LONG,MPI_SUM,world);
		if (force->newton_bond == 0) atom->ndihedrals /= 4;
		}

		if (atom->avec->impropers_allow) {
		int nimpropers = 0;
		bigint nimpropers = 0;
		for (i = 0; i < nlocal; i++) nimpropers += atom->num_improper[i];
		MPI_Allreduce(&nimpropers,&atom->nimpropers,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&nimpropers,&atom->nimpropers,
		1,MPI_UNSIGNED_LONG,MPI_SUM,world);
		if (force->newton_bond == 0) atom->nimpropers /= 4;
		}

		@@ -370,11 +372,11 @@ void DeleteBonds::command(int narg, char **arg)

		// compute and print stats

		int tmp;
		int bond_on,bond_off;
		int angle_on,angle_off;
		int dihedral_on,dihedral_off;
		int improper_on,improper_off;
		bigint tmp;
		bigint bond_on,bond_off;
		bigint angle_on,angle_off;
		bigint dihedral_on,dihedral_off;
		bigint improper_on,improper_off;

		if (atom->avec->bonds_allow) {
		bond_on = bond_off = 0;
		@@ -382,9 +384,9 @@ void DeleteBonds::command(int narg, char **arg)
		for (m = 0; m < atom->num_bond[i]; m++)
		if (atom->bond_type[i][m] > 0) bond_on++;
		else bond_off++;
		MPI_Allreduce(&bond_on,&tmp,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&bond_on,&tmp,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
		bond_on = tmp;
		MPI_Allreduce(&bond_off,&tmp,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&bond_off,&tmp,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
		bond_off = tmp;
		if (force->newton_bond == 0) {
		bond_on /= 2;
		@@ -398,9 +400,9 @@ void DeleteBonds::command(int narg, char **arg)
		for (m = 0; m < atom->num_angle[i]; m++)
		if (atom->angle_type[i][m] > 0) angle_on++;
		else angle_off++;
		MPI_Allreduce(&angle_on,&tmp,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&angle_on,&tmp,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
		angle_on = tmp;
		MPI_Allreduce(&angle_off,&tmp,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&angle_off,&tmp,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
		angle_off = tmp;
		if (force->newton_bond == 0) {
		angle_on /= 3;
		@@ -414,9 +416,9 @@ void DeleteBonds::command(int narg, char **arg)
		for (m = 0; m < atom->num_dihedral[i]; m++)
		if (atom->dihedral_type[i][m] > 0) dihedral_on++;
		else dihedral_off++;
		MPI_Allreduce(&dihedral_on,&tmp,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&dihedral_on,&tmp,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
		dihedral_on = tmp;
		MPI_Allreduce(&dihedral_off,&tmp,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&dihedral_off,&tmp,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
		dihedral_off = tmp;
		if (force->newton_bond == 0) {
		dihedral_on /= 4;
		@@ -430,9 +432,9 @@ void DeleteBonds::command(int narg, char **arg)
		for (m = 0; m < atom->num_improper[i]; m++)
		if (atom->improper_type[i][m] > 0) improper_on++;
		else improper_off++;
		MPI_Allreduce(&improper_on,&tmp,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&improper_on,&tmp,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
		improper_on = tmp;
		MPI_Allreduce(&improper_off,&tmp,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&improper_off,&tmp,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
		improper_off = tmp;
		if (force->newton_bond == 0) {
		improper_on /= 4;
		@@ -443,30 +445,32 @@ void DeleteBonds::command(int narg, char **arg)
		if (comm->me == 0) {
		if (screen) {
		if (atom->avec->bonds_allow)
		fprintf(screen," %d total bonds, %d turned on, %d turned off\n",
		fprintf(screen," %lu total bonds, %lu turned on, %lu turned off\n",
		atom->nbonds,bond_on,bond_off);
		if (atom->avec->angles_allow)
		fprintf(screen," %d total angles, %d turned on, %d turned off\n",
		fprintf(screen," %lu total angles, %lu turned on, %lu turned off\n",
		atom->nangles,angle_on,angle_off);
		if (atom->avec->dihedrals_allow)
		fprintf(screen," %d total dihedrals, %d turned on, %d turned off\n",
		fprintf(screen," %lu total dihedrals, %lu turned on, %lu turned off\n",
		atom->ndihedrals,dihedral_on,dihedral_off);
		if (atom->avec->impropers_allow)
		fprintf(screen," %d total impropers, %d turned on, %d turned off\n",
		fprintf(screen," %lu total impropers, %lu turned on, %lu turned off\n",
		atom->nimpropers,improper_on,improper_off);
		}
		if (logfile) {
		if (atom->avec->bonds_allow)
		fprintf(logfile," %d total bonds, %d turned on, %d turned off\n",
		fprintf(logfile," %lu total bonds, %lu turned on, %lu turned off\n",
		atom->nbonds,bond_on,bond_off);
		if (atom->avec->angles_allow)
		fprintf(logfile," %d total angles, %d turned on, %d turned off\n",
		fprintf(logfile," %lu total angles, %lu turned on, %lu turned off\n",
		atom->nangles,angle_on,angle_off);
		if (atom->avec->dihedrals_allow)
		fprintf(logfile," %d total dihedrals, %d turned on, %d turned off\n",
		fprintf(logfile," %lu total dihedrals, %lu turned on, "
		"%lu turned off\n",
		atom->ndihedrals,dihedral_on,dihedral_off);
		if (atom->avec->impropers_allow)
		fprintf(logfile," %d total impropers, %d turned on, %d turned off\n",
		fprintf(logfile," %lu total impropers, %lu turned on, "
		"%lu turned off\n",
		atom->nimpropers,improper_on,improper_off);
		}
		}

src/read_data.cpp

+54 −47

Original line number	Diff line number	Diff line
		@@ -337,10 +337,10 @@ void ReadData::header(int flag)
		// search line for header keyword and set corresponding variable

		if (strstr(line,"atoms")) sscanf(line,"%lu",&atom->natoms);
		else if (strstr(line,"bonds")) sscanf(line,"%d",&atom->nbonds);
		else if (strstr(line,"angles")) sscanf(line,"%d",&atom->nangles);
		else if (strstr(line,"dihedrals")) sscanf(line,"%d",&atom->ndihedrals);
		else if (strstr(line,"impropers")) sscanf(line,"%d",&atom->nimpropers);
		else if (strstr(line,"bonds")) sscanf(line,"%lu",&atom->nbonds);
		else if (strstr(line,"angles")) sscanf(line,"%lu",&atom->nangles);
		else if (strstr(line,"dihedrals")) sscanf(line,"lu",&atom->ndihedrals);
		else if (strstr(line,"impropers")) sscanf(line,"%lu",&atom->nimpropers);

		else if (strstr(line,"atom types")) sscanf(line,"%d",&atom->ntypes);
		else if (strstr(line,"bond types")) sscanf(line,"%d",&atom->nbondtypes);
		@@ -434,12 +434,12 @@ void ReadData::atoms()

		// check that all atoms were assigned correctly

		double tmp = atom->nlocal;
		MPI_Allreduce(&tmp,&natoms,1,MPI_DOUBLE,MPI_SUM,world);
		bigint tmp = atom->nlocal;
		MPI_Allreduce(&tmp,&natoms,1,MPI_UNSIGNED_LONG,MPI_SUM,world);

		if (me == 0) {
		if (screen) fprintf(screen," %.15g atoms\n",natoms);
		if (logfile) fprintf(logfile," %.15g atoms\n",natoms);
		if (screen) fprintf(screen," %lu atoms\n",natoms);
		if (logfile) fprintf(logfile," %lu atoms\n",natoms);
		}

		if (natoms != atom->natoms) error->all("Did not assign all atoms correctly");
		@@ -529,8 +529,8 @@ void ReadData::velocities()
		}

		if (me == 0) {
		if (screen) fprintf(screen," %.15g velocities\n",natoms);
		if (logfile) fprintf(logfile," %.15g velocities\n",natoms);
		if (screen) fprintf(screen," %lu velocities\n",natoms);
		if (logfile) fprintf(logfile," %lu velocities\n",natoms);
		}
		}

		@@ -540,9 +540,11 @@ void ReadData::bonds()
		{
		int i,m,nchunk;

		int nread = 0;
		while (nread < atom->nbonds) {
		nchunk = MIN(atom->nbonds-nread,CHUNK);
		bigint nread = 0;
		bigint nbonds = atom->nbonds;

		while (nread < nbonds) {
		nchunk = MIN(nbonds-nread,CHUNK);
		if (me == 0) {
		char *eof;
		m = 0;
		@@ -563,17 +565,16 @@ void ReadData::bonds()
		// check that bonds were assigned correctly

		int nlocal = atom->nlocal;

		int sum;
		int n = 0;
		bigint sum;
		bigint n = 0;
		for (i = 0; i < nlocal; i++) n += atom->num_bond[i];
		MPI_Allreduce(&n,&sum,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&n,&sum,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
		int factor = 1;
		if (!force->newton_bond) factor = 2;

		if (me == 0) {
		if (screen) fprintf(screen," %d bonds\n",sum/factor);
		if (logfile) fprintf(logfile," %d bonds\n",sum/factor);
		if (screen) fprintf(screen," %lu bonds\n",sum/factor);
		if (logfile) fprintf(logfile," %lu bonds\n",sum/factor);
		}
		if (sum != factor*atom->nbonds) error->all("Bonds assigned incorrectly");
		}
		@@ -584,9 +585,11 @@ void ReadData::angles()
		{
		int i,m,nchunk;

		int nread = 0;
		while (nread < atom->nangles) {
		nchunk = MIN(atom->nangles-nread,CHUNK);
		bigint nread = 0;
		bigint nangles = atom->nangles;

		while (nread < nangles) {
		nchunk = MIN(nangles-nread,CHUNK);
		if (me == 0) {
		char *eof;
		m = 0;
		@@ -604,20 +607,19 @@ void ReadData::angles()
		nread += nchunk;
		}

		// check that angles were assigned correctly
		// check that ang

		int nlocal = atom->nlocal;

		int sum;
		int n = 0;
		bigint sum;
		bigint n = 0;
		for (i = 0; i < nlocal; i++) n += atom->num_angle[i];
		MPI_Allreduce(&n,&sum,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&n,&sum,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
		int factor = 1;
		if (!force->newton_bond) factor = 3;

		if (me == 0) {
		if (screen) fprintf(screen," %d angles\n",sum/factor);
		if (logfile) fprintf(logfile," %d angles\n",sum/factor);
		if (screen) fprintf(screen," %lu angles\n",sum/factor);
		if (logfile) fprintf(logfile," %lu angles\n",sum/factor);
		}
		if (sum != factor*atom->nangles) error->all("Angles assigned incorrectly");
		}
		@@ -628,9 +630,11 @@ void ReadData::dihedrals()
		{
		int i,m,nchunk;

		int nread = 0;
		while (nread < atom->ndihedrals) {
		nchunk = MIN(atom->ndihedrals-nread,CHUNK);
		bigint nread = 0;
		bigint ndihedrals = atom->ndihedrals;

		while (nread < ndihedrals) {
		nchunk = MIN(ndihedrals-nread,CHUNK);
		if (me == 0) {
		char *eof;
		m = 0;
		@@ -651,17 +655,16 @@ void ReadData::dihedrals()
		// check that dihedrals were assigned correctly

		int nlocal = atom->nlocal;

		int sum;
		int n = 0;
		bigint sum;
		bigint n = 0;
		for (i = 0; i < nlocal; i++) n += atom->num_dihedral[i];
		MPI_Allreduce(&n,&sum,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&n,&sum,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
		int factor = 1;
		if (!force->newton_bond) factor = 4;

		if (me == 0) {
		if (screen) fprintf(screen," %d dihedrals\n",sum/factor);
		if (logfile) fprintf(logfile," %d dihedrals\n",sum/factor);
		if (screen) fprintf(screen," %lu dihedrals\n",sum/factor);
		if (logfile) fprintf(logfile," %lu dihedrals\n",sum/factor);
		}
		if (sum != factor*atom->ndihedrals)
		error->all("Dihedrals assigned incorrectly");
		@@ -673,9 +676,11 @@ void ReadData::impropers()
		{
		int i,m,nchunk;

		int nread = 0;
		while (nread < atom->nimpropers) {
		nchunk = MIN(atom->nimpropers-nread,CHUNK);
		bigint nread = 0;
		bigint nimpropers = atom->nimpropers;

		while (nread < nimpropers) {
		nchunk = MIN(nread,CHUNK);
		if (me == 0) {
		char *eof;
		m = 0;
		@@ -696,17 +701,16 @@ void ReadData::impropers()
		// check that impropers were assigned correctly

		int nlocal = atom->nlocal;

		int sum;
		int n = 0;
		bigint sum;
		bigint n = 0;
		for (i = 0; i < nlocal; i++) n += atom->num_improper[i];
		MPI_Allreduce(&n,&sum,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&n,&sum,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
		int factor = 1;
		if (!force->newton_bond) factor = 4;

		if (me == 0) {
		if (screen) fprintf(screen," %d impropers\n",sum/factor);
		if (logfile) fprintf(logfile," %d impropers\n",sum/factor);
		if (screen) fprintf(screen," %lu impropers\n",sum/factor);
		if (logfile) fprintf(logfile," %lu impropers\n",sum/factor);
		}
		if (sum != factor*atom->nimpropers)
		error->all("Impropers assigned incorrectly");
		@@ -972,6 +976,9 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
		int i,tmp1,tmp2,atom1,atom2,atom3,atom4;
		char *eof;

		if (atom->natoms > MAXINT32)
		error->all("Molecular data file has too many atoms");

		int natoms = static_cast<int> (atom->natoms);
		bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;

src/read_restart.cpp

+12 −12

Original line number	Diff line number	Diff line
		@@ -304,20 +304,20 @@ void ReadRestart::command(int narg, char **arg)

		if (me == 0) {
		if (atom->nbonds) {
		if (screen) fprintf(screen," %d bonds\n",atom->nbonds);
		if (logfile) fprintf(logfile," %d bonds\n",atom->nbonds);
		if (screen) fprintf(screen," %lu bonds\n",atom->nbonds);
		if (logfile) fprintf(logfile," %lu bonds\n",atom->nbonds);
		}
		if (atom->nangles) {
		if (screen) fprintf(screen," %d angles\n",atom->nangles);
		if (logfile) fprintf(logfile," %d angles\n",atom->nangles);
		if (screen) fprintf(screen," %lu angles\n",atom->nangles);
		if (logfile) fprintf(logfile," %lu angles\n",atom->nangles);
		}
		if (atom->ndihedrals) {
		if (screen) fprintf(screen," %d dihedrals\n",atom->ndihedrals);
		if (logfile) fprintf(logfile," %d dihedrals\n",atom->ndihedrals);
		if (screen) fprintf(screen," %lu dihedrals\n",atom->ndihedrals);
		if (logfile) fprintf(logfile," %lu dihedrals\n",atom->ndihedrals);
		}
		if (atom->nimpropers) {
		if (screen) fprintf(screen," %d impropers\n",atom->nimpropers);
		if (logfile) fprintf(logfile," %d impropers\n",atom->nimpropers);
		if (screen) fprintf(screen," %lu impropers\n",atom->nimpropers);
		if (logfile) fprintf(logfile," %lu impropers\n",atom->nimpropers);
		}
		}

		@@ -599,25 +599,25 @@ void ReadRestart::header()
		} else if (flag == NTYPES) {
		atom->ntypes = read_int();
		} else if (flag == NBONDS) {
		atom->nbonds = read_int();
		atom->nbonds = read_bigint();
		} else if (flag == NBONDTYPES) {
		atom->nbondtypes = read_int();
		} else if (flag == BOND_PER_ATOM) {
		atom->bond_per_atom = read_int();
		} else if (flag == NANGLES) {
		atom->nangles = read_int();
		atom->nangles = read_bigint();
		} else if (flag == NANGLETYPES) {
		atom->nangletypes = read_int();
		} else if (flag == ANGLE_PER_ATOM) {
		atom->angle_per_atom = read_int();
		} else if (flag == NDIHEDRALS) {
		atom->ndihedrals = read_int();
		atom->ndihedrals = read_bigint();
		} else if (flag == NDIHEDRALTYPES) {
		atom->ndihedraltypes = read_int();
		} else if (flag == DIHEDRAL_PER_ATOM) {
		atom->dihedral_per_atom = read_int();
		} else if (flag == NIMPROPERS) {
		atom->nimpropers = read_int();
		atom->nimpropers = read_bigint();
		} else if (flag == NIMPROPERTYPES) {
		atom->nimpropertypes = read_int();
		} else if (flag == IMPROPER_PER_ATOM) {

src/write_restart.cpp

+4 −4

Original line number	Diff line number	Diff line
		@@ -334,16 +334,16 @@ void WriteRestart::header()

		write_bigint(NATOMS,natoms);
		write_int(NTYPES,atom->ntypes);
		write_int(NBONDS,atom->nbonds);
		write_bigint(NBONDS,atom->nbonds);
		write_int(NBONDTYPES,atom->nbondtypes);
		write_int(BOND_PER_ATOM,atom->bond_per_atom);
		write_int(NANGLES,atom->nangles);
		write_bigint(NANGLES,atom->nangles);
		write_int(NANGLETYPES,atom->nangletypes);
		write_int(ANGLE_PER_ATOM,atom->angle_per_atom);
		write_int(NDIHEDRALS,atom->ndihedrals);
		write_bigint(NDIHEDRALS,atom->ndihedrals);
		write_int(NDIHEDRALTYPES,atom->ndihedraltypes);
		write_int(DIHEDRAL_PER_ATOM,atom->dihedral_per_atom);
		write_int(NIMPROPERS,atom->nimpropers);
		write_bigint(NIMPROPERS,atom->nimpropers);
		write_int(NIMPROPERTYPES,atom->nimpropertypes);
		write_int(IMPROPER_PER_ATOM,atom->improper_per_atom);

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