diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index b5daa6416e..2ea1da3db3 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -16,7 +16,8 @@ dump-ID = ID of dump to modify :ulb,l one or more keyword/value pairs may be appended :l these keywords apply to various dump styles :l keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l - {append} arg = {yes} or {no} + {append} arg = {yes} or {no} or {at} N + N = index of frame written upon first dump {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 @@ -41,6 +42,7 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o {region} arg = region-ID or "none" {scale} arg = {yes} or {no} {sfactor} arg = coordinate scaling factor (> 0.0) + {thermo} arg = {yes} or {no} {tfactor} arg = time scaling factor (> 0.0) {sort} arg = {off} or {id} or N or -N off = no sorting of per-atom lines within a snapshot @@ -139,12 +141,13 @@ 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. 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. 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. :line @@ -413,6 +416,13 @@ most effective when the typical magnitude of position data is between :line +The {thermo} keyword ({netcdf} only) triggers writing of "thermo"_thermo.html +information to the dump file alongside per-atom data. The data included in the +dump file is identical to the data specified by +"thermo_style"_thermo_style.html. + +:line + The {region} keyword only applies to the dump {custom}, {cfg}, {image}, and {movie} styles. If specified, only atoms in the region will be written to the dump file or included in the image/movie. Only diff --git a/doc/src/dump_netcdf.txt b/doc/src/dump_netcdf.txt index 4e82656698..63568137a6 100644 --- a/doc/src/dump_netcdf.txt +++ b/doc/src/dump_netcdf.txt @@ -24,7 +24,7 @@ args = list of atom attributes, same as for "dump_style custom"_dump.html :l,ule [Examples:] dump 1 all netcdf 100 traj.nc type x y z vx vy vz -dump_modify 1 append yes at -1 global c_thermo_pe c_thermo_temp c_thermo_press +dump_modify 1 append yes at -1 thermo yes dump 1 all netcdf/mpiio 1000 traj.nc id type x y z :pre [Description:] @@ -44,7 +44,7 @@ rank. NetCDF files can be directly visualized via the following tools: Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and -all of the above extensions. :ule,b +all extensions of this dump style. :ule,b VMD (http://www.ks.uiuc.edu/Research/vmd/). :l @@ -52,15 +52,9 @@ AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains a NetCDF reader that is not present in the standard distribution of AtomEye. :l,ule -In addition to per-atom data, global data can be included in the dump -file, which are the kinds of values output by the -"thermo_style"_thermo_style.html command . See "Section howto -6.15"_Section_howto.html#howto_15 for an explanation of per-atom -versus global data. The global output written into the dump file can -be from computes, fixes, or variables, by prefixing the compute/fix ID -or variable name with "c_" or "f_" or "v_" respectively, as in the -example above. These global values are specified via the "dump_modify -global"_dump_modify.html command. +In addition to per-atom data, "thermo"_thermo.html data can be included in the +dump file. The data included in the dump file is identical to the data specified +by "thermo_style"_thermo_style.html. :link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/) :link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)