Merge pull request #681 from lammps/dump-modify (a1f5693f) · Commits · 郑智淋 / lammps

doc/src/Section_commands.txt

+14 −14

Original line number	Diff line number	Diff line
		@@ -917,9 +917,9 @@ KOKKOS, o = USER-OMP, t = OPT.
		"born/coul/wolf (go)"_pair_born.html,
		"brownian (o)"_pair_brownian.html,
		"brownian/poly (o)"_pair_brownian.html,
		"buck (gkio)"_pair_buck.html,
		"buck/coul/cut (gkio)"_pair_buck.html,
		"buck/coul/long (gkio)"_pair_buck.html,
		"buck (giko)"_pair_buck.html,
		"buck/coul/cut (giko)"_pair_buck.html,
		"buck/coul/long (giko)"_pair_buck.html,
		"buck/coul/long/cs"_pair_buck.html,
		"buck/coul/msm (o)"_pair_buck.html,
		"buck/long/coul/long (o)"_pair_buck_long.html,
		@@ -934,12 +934,12 @@ KOKKOS, o = USER-OMP, t = OPT.
		"coul/msm"_pair_coul.html,
		"coul/streitz"_pair_coul.html,
		"coul/wolf (ko)"_pair_coul.html,
		"dpd (go)"_pair_dpd.html,
		"dpd (gio)"_pair_dpd.html,
		"dpd/tstat (go)"_pair_dpd.html,
		"dsmc"_pair_dsmc.html,
		"eam (gkiot)"_pair_eam.html,
		"eam/alloy (gkiot)"_pair_eam.html,
		"eam/fs (gkiot)"_pair_eam.html,
		"eam (gikot)"_pair_eam.html,
		"eam/alloy (gikot)"_pair_eam.html,
		"eam/fs (gikot)"_pair_eam.html,
		"eim (o)"_pair_eim.html,
		"gauss (go)"_pair_gauss.html,
		"gayberne (gio)"_pair_gayberne.html,
		@@ -953,9 +953,9 @@ KOKKOS, o = USER-OMP, t = OPT.
		"kim"_pair_kim.html,
		"lcbop"_pair_lcbop.html,
		"line/lj"_pair_line_lj.html,
		"lj/charmm/coul/charmm (kio)"_pair_charmm.html,
		"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
		"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
		"lj/charmm/coul/long (gkio)"_pair_charmm.html,
		"lj/charmm/coul/long (giko)"_pair_charmm.html,
		"lj/charmm/coul/msm"_pair_charmm.html,
		"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
		"lj/charmmfsw/coul/long"_pair_charmm.html,
		@@ -1005,9 +1005,9 @@ KOKKOS, o = USER-OMP, t = OPT.
		"resquared (go)"_pair_resquared.html,
		"snap"_pair_snap.html,
		"soft (go)"_pair_soft.html,
		"sw (gkio)"_pair_sw.html,
		"sw (giko)"_pair_sw.html,
		"table (gko)"_pair_table.html,
		"tersoff (gkio)"_pair_tersoff.html,
		"tersoff (giko)"_pair_tersoff.html,
		"tersoff/mod (gko)"_pair_tersoff_mod.html,
		"tersoff/mod/c (o)"_pair_tersoff_mod.html,
		"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
		@@ -1177,7 +1177,7 @@ USER-OMP, t = OPT.
		"none"_dihedral_none.html,
		"zero"_dihedral_zero.html,
		"hybrid"_dihedral_hybrid.html,
		"charmm (ko)"_dihedral_charmm.html,
		"charmm (iko)"_dihedral_charmm.html,
		"charmmfsw"_dihedral_charmm.html,
		"class2 (ko)"_dihedral_class2.html,
		"harmonic (io)"_dihedral_harmonic.html,
		@@ -1190,7 +1190,7 @@ used if "LAMMPS is built with the appropriate
		package"_Section_start.html#start_3.

		"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
		"fourier (o)"_dihedral_fourier.html,
		"fourier (io)"_dihedral_fourier.html,
		"nharmonic (o)"_dihedral_nharmonic.html,
		"quadratic (o)"_dihedral_quadratic.html,
		"spherical (o)"_dihedral_spherical.html,
		@@ -1213,7 +1213,7 @@ USER-OMP, t = OPT.
		"hybrid"_improper_hybrid.html,
		"class2 (ko)"_improper_class2.html,
		"cvff (io)"_improper_cvff.html,
		"harmonic (ko)"_improper_harmonic.html,
		"harmonic (iko)"_improper_harmonic.html,
		"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

		These are additional improper styles in USER packages, which can be

doc/src/dump_modify.txt

+12 −8

Original line number	Diff line number	Diff line
		@@ -19,7 +19,6 @@ keyword = {append} or {at} or {buffer} or {element} or {every} or {fileper} or {
		{append} arg = {yes} or {no}
		{at} arg = N
		N = index of frame written upon first dump
		only available after "append yes"
		{buffer} arg = {yes} or {no}
		{element} args = E1 E2 ... EN, where N = # of atom types
		E1,...,EN = element name, e.g. C or Fe or Ga
		@@ -143,13 +142,18 @@ and {dcd}. It also applies only to text output files, not to binary
		or gzipped or image/movie files. If specified as {yes}, then dump
		snapshots are appended to the end of an existing dump file. If
		specified as {no}, then a new dump file will be created which will
		overwrite an existing file with the same name. If the {at} option is present
		({netcdf} only), then the frame to append to can be specified. Negative values
		are counted from the end of the file. This keyword can only take effect if the
		dump_modify command is used after the "dump"_dump.html command, but before the
		first command that causes dump snapshots to be output, e.g. a "run"_run.html or
		"minimize"_minimize.html command. Once the dump file has been opened, this
		keyword has no further effect.
		overwrite an existing file with the same name.

		:line

		The {at} keyword only applies to the {netcdf} dump style. It can only
		be used if the {append yes} keyword is also used. The {N} argument is
		the index of which frame to append to. A negative value can be
		specified for {N}, which means a frame counted from the end of the
		file. The {at} keyword can only be used if the dump_modify command is
		before the first command that causes dump snapshots to be output,
		e.g. a "run"_run.html or "minimize"_minimize.html command. Once the
		dump file has been opened, this keyword has no further effect.

		:line

src/USER-NETCDF/dump_netcdf.cpp

+11 −8

Original line number	Diff line number	Diff line
		@@ -330,8 +330,7 @@ void DumpNetCDF::openfile()
		// Type mangling
		if (vtype[perat[i].field[0]] == INT) {
		xtype = NC_INT;
		}
		else {
		} else {
		if (double_precision)
		xtype = NC_DOUBLE;
		else
		@@ -355,10 +354,13 @@ void DumpNetCDF::openfile()
		NCERR( nc_inq_dimlen(ncid, frame_dim, &nframes) );
		// framei == -1 means append to file, == -2 means override last frame
		// Note that in the input file this translates to 'yes', '-1', etc.
		if (framei < 0 \|\| (append_flag && framei == 0)) framei = nframes+framei+1;

		if (framei <= 0) framei = nframes+framei+1;
		if (framei < 1) framei = 1;
		}
		else {
		} else {
		if (framei != 0)
		error->all(FLERR,"at keyword requires use of 'append yes'");

		int dims[NC_MAX_VAR_DIMS];
		size_t index[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
		double d[1];
		@@ -924,11 +926,12 @@ int DumpNetCDF::modify_param(int narg, char **arg)
		return 2;
		}
		else if (strcmp(arg[iarg],"at") == 0) {
		if (!append_flag)
		error->all(FLERR,"expected 'append yes' before 'at' keyword");
		iarg++;
		if (iarg >= narg)
		error->all(FLERR,"expected additional arg after 'at' keyword.");
		framei = force->inumeric(FLERR,arg[iarg]);
		if (framei < 0) framei--;
		if (framei == 0) error->all(FLERR,"frame 0 not allowed for 'at' keyword.");
		else if (framei < 0) framei--;
		iarg++;
		return 2;
		}

src/USER-NETCDF/dump_netcdf_mpiio.cpp

+9 −6

Original line number	Diff line number	Diff line
		@@ -351,10 +351,12 @@ void DumpNetCDFMPIIO::openfile()
		NCERR( ncmpi_inq_dimlen(ncid, frame_dim, &nframes) );
		// framei == -1 means append to file, == -2 means override last frame
		// Note that in the input file this translates to 'yes', '-1', etc.
		if (framei < 0 \|\| (append_flag && framei == 0)) framei = nframes+framei+1;
		if (framei <= 0) framei = nframes+framei+1;
		if (framei < 1) framei = 1;
		}
		else {
		} else {
		if (framei != 0)
		error->all(FLERR,"at keyword requires use of 'append yes'");

		int dims[NC_MAX_VAR_DIMS];
		MPI_Offset index[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
		double d[1];
		@@ -920,11 +922,12 @@ int DumpNetCDFMPIIO::modify_param(int narg, char **arg)
		return 2;
		}
		else if (strcmp(arg[iarg],"at") == 0) {
		if (!append_flag)
		error->all(FLERR,"expected 'append yes' before 'at' keyword");
		iarg++;
		if (iarg >= narg)
		error->all(FLERR,"expected additional arg after 'at' keyword.");
		framei = force->inumeric(FLERR,arg[iarg]);
		if (framei < 0) framei--;
		if (framei == 0) error->all(FLERR,"frame 0 not allowed for 'at' keyword.");
		else if (framei < 0) framei--;
		iarg++;
		return 2;
		}

src/modify.cpp

+1 −2

Original line number	Diff line number	Diff line
		@@ -949,8 +949,7 @@ void Modify::delete_fix(const char *id)

		void Modify::delete_fix(int ifix)
		{
		if(fix[ifix])
		delete fix[ifix];
		if (fix[ifix]) delete fix[ifix];
		atom->update_callback(ifix);

		// move other Fixes and fmask down in list one slot

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