From 397f967521f43ea21ca87b85288b40fa2dd4e8c9 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 6 Oct 2010 15:58:26 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4978 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_errors.html | 4 ++++ doc/Section_errors.txt | 4 ++++ doc/dump.html | 29 +++++++++++++++-------------- doc/dump.txt | 29 +++++++++++++++-------------- 4 files changed, 38 insertions(+), 28 deletions(-) diff --git a/doc/Section_errors.html b/doc/Section_errors.html index 9de94acb9f..22eff1ad29 100644 --- a/doc/Section_errors.html +++ b/doc/Section_errors.html @@ -596,6 +596,10 @@ fix/deform are defined .
The frequency of writing dump dcd snapshots cannot be changed. +
Cannot change dump_modify every for dump xtc + +
The frequency of writing dump xtc snapshots cannot be changed. +
Cannot change timestep once fix srd is setup
This is because various SRD properties depend on the timestep diff --git a/doc/Section_errors.txt b/doc/Section_errors.txt index 1783af069d..9bfdffc9df 100644 --- a/doc/Section_errors.txt +++ b/doc/Section_errors.txt @@ -593,6 +593,10 @@ Self-explanatory. :dd The frequency of writing dump dcd snapshots cannot be changed. :dd +{Cannot change dump_modify every for dump xtc} :dt + +The frequency of writing dump xtc snapshots cannot be changed. :dd + {Cannot change timestep once fix srd is setup} :dt This is because various SRD properties depend on the timestep diff --git a/doc/dump.html b/doc/dump.html index b0afc59733..f4601e1579 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -200,21 +200,22 @@ files are binary and thus may not be portable to different machines. The number of atoms per snapshot cannot change with the dcd style. The unwrap option of the dump_modify command allows DCD coordinates to be written "unwrapped" by the image flags -for each atom. Unwrapped means that if the atom has passed thru a -periodic boundary one or more times, the value is printed for what the -coordinate would be if it had not been wrapped back into the periodic -box. Note that these coordinates may thus be far outside the box size -stored with the snapshot. +for each atom. Unwrapped means that if the atom has passed through +a periodic boundary one or more times, the value is printed for what +the coordinate would be if it had not been wrapped back into the +periodic box. Note that these coordinates may thus be far outside +the box size stored with the snapshot.

The xtc style writes XTC files, a compressed trajectory format used by the GROMACS molecular dynamics package, and described -here. +here. The precision used in XTC files can be adjusted via the dump_modify command. The default value of 1000 means that coordinates are stored to 1/1000 nanometer accuracy. XTC -files are portable binary files written in the NFS XDR data format, so -that any machine which supports XDR should be able to read them. The -unwrap option of the dump_modify command allows +files are portable binary files written in the NFS XDR data format, +so that any machine which supports XDR should be able to read them. +The number of atoms per snapshot cannot change with the xtc style. +The unwrap option of the dump_modify command allows XTC coordinates to be written "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has passed thru a periodic boundary one or more times, the value is printed for what the @@ -449,18 +450,18 @@ section of the documentation.

The xtc style is part of the "xtc" package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info. This is because -some machines may not support the lo-level XDR data format that XTC +some machines may not support the low-level XDR data format that XTC files are written with, which will result in a compile-time error when -a lo-level include file is not found. Putting this style in a package +a low-level include file is not found. Putting this style in a package makes it easy to exclude from a LAMMPS build for those machines. However, the XTC package also includes two compatibility header files and associated functions, which should be a suitable substitute on machines that do not have the appropriate native header files. This option can be invoked at build time by adding -DLAMMPS_XDR to the -CCFLAGS variable in the appropriate lo-level Makefile, +CCFLAGS variable in the appropriate low-level Makefile, e.g. src/MAKE/Makefile.foo. This compatibility mode has been tested -successfully on Cray XT3 and IBM BlueGene/L machines and should also -work on the Cray XT4, IBM BG/P, and Windows XP machines. +successfully on Cray XT3/XT4/XT5 and IBM BlueGene/L machines and +should also work on IBM BG/P, and Windows XP/Vista/7 machines.

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diff --git a/doc/dump.txt b/doc/dump.txt index 4d5091b995..508e7fc47b 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -190,21 +190,22 @@ files are binary and thus may not be portable to different machines. The number of atoms per snapshot cannot change with the {dcd} style. The {unwrap} option of the "dump_modify"_dump_modify.html command allows DCD coordinates to be written "unwrapped" by the image flags -for each atom. Unwrapped means that if the atom has passed thru a -periodic boundary one or more times, the value is printed for what the -coordinate would be if it had not been wrapped back into the periodic -box. Note that these coordinates may thus be far outside the box size -stored with the snapshot. +for each atom. Unwrapped means that if the atom has passed through +a periodic boundary one or more times, the value is printed for what +the coordinate would be if it had not been wrapped back into the +periodic box. Note that these coordinates may thus be far outside +the box size stored with the snapshot. The {xtc} style writes XTC files, a compressed trajectory format used by the GROMACS molecular dynamics package, and described -"here"_http://www.gromacs.org/documentation/reference_3.3/online/xtc.html. +"here"_http://manual.gromacs.org/current/online/xtc.html. The precision used in XTC files can be adjusted via the "dump_modify"_dump_modify.html command. The default value of 1000 means that coordinates are stored to 1/1000 nanometer accuracy. XTC -files are portable binary files written in the NFS XDR data format, so -that any machine which supports XDR should be able to read them. The -{unwrap} option of the "dump_modify"_dump_modify.html command allows +files are portable binary files written in the NFS XDR data format, +so that any machine which supports XDR should be able to read them. +The number of atoms per snapshot cannot change with the {xtc} style. +The {unwrap} option of the "dump_modify"_dump_modify.html command allows XTC coordinates to be written "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has passed thru a periodic boundary one or more times, the value is printed for what the @@ -439,18 +440,18 @@ section of the documentation. The {xtc} style is part of the "xtc" package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. This is because -some machines may not support the lo-level XDR data format that XTC +some machines may not support the low-level XDR data format that XTC files are written with, which will result in a compile-time error when -a lo-level include file is not found. Putting this style in a package +a low-level include file is not found. Putting this style in a package makes it easy to exclude from a LAMMPS build for those machines. However, the XTC package also includes two compatibility header files and associated functions, which should be a suitable substitute on machines that do not have the appropriate native header files. This option can be invoked at build time by adding -DLAMMPS_XDR to the -CCFLAGS variable in the appropriate lo-level Makefile, +CCFLAGS variable in the appropriate low-level Makefile, e.g. src/MAKE/Makefile.foo. This compatibility mode has been tested -successfully on Cray XT3 and IBM BlueGene/L machines and should also -work on the Cray XT4, IBM BG/P, and Windows XP machines. +successfully on Cray XT3/XT4/XT5 and IBM BlueGene/L machines and +should also work on IBM BG/P, and Windows XP/Vista/7 machines. [Related commands:]