diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 0d46a01424ff0c986e5f9137b995a65ab11cbc3a..da1121e811dbd076d230d3ecc1914a13bf143b5a 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -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 diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index 38d9aad4d95ef962e8aa08e8d4bc9c75ae2442fc..db727c2d4f7bdec779f196524a71a7dfd2ea3193 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -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 diff --git a/src/USER-NETCDF/dump_netcdf.cpp b/src/USER-NETCDF/dump_netcdf.cpp index a9532d10775ff0e5ffb71d55d4b0841389c30af1..57404e40d604f921cabbc0d1f1b7ff7737a75285 100644 --- a/src/USER-NETCDF/dump_netcdf.cpp +++ b/src/USER-NETCDF/dump_netcdf.cpp @@ -355,7 +355,12 @@ 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 (!append_flag) + error->all(FLERR,"at keyword requires use of 'append yes'"); + + if (framei < 0 || (append_flag && framei == 0)) + framei = nframes+framei+1; if (framei < 1) framei = 1; } else { @@ -924,11 +929,11 @@ 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) framei--; iarg++; return 2; } diff --git a/src/modify.cpp b/src/modify.cpp index 361079bc16d67c8c8127e56c4ad0928d4a073945..04137f110a5ae96779ea395b9af68ad6380db5b8 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -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