Merge pull request #681 from lammps/dump-modify

remove dependence of dump modify 'at' and 'append'

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 (giko)"_pair_buck.html,
-"buck/coul/cut (gkio)"_pair_buck.html,
+"buck/coul/cut (giko)"_pair_buck.html,
-"buck/coul/long (gkio)"_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 (gikot)"_pair_eam.html,
-"eam/alloy (gkiot)"_pair_eam.html,
+"eam/alloy (gikot)"_pair_eam.html,
-"eam/fs (gkiot)"_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

@@ -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
+overwrite an existing file with the same name.
-({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
+:line
-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
+The {at} keyword only applies to the {netcdf} dump style.  It can only
-"minimize"_minimize.html command.  Once the dump file has been opened, this
+be used if the {append yes} keyword is also used.  The {N} argument is
-keyword has no further effect.
+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

@@ -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

@@ -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

@@ -949,8 +949,7 @@ void Modify::delete_fix(const char *id)
 
 void Modify::delete_fix(int ifix)
 {
-  if(fix[ifix])
+  if (fix[ifix]) delete fix[ifix];
-    delete fix[ifix];
   atom->update_callback(ifix);
 
   // move other Fixes and fmask down in list one slot