(8) The DEPFLAGS setting is how the C++ compiler creates a dependency file for each source file. This speeds re-compilation when source diff --git a/doc/Section_start.txt b/doc/Section_start.txt index 3c508789d4..7aaa0f8b9b 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -185,7 +185,11 @@ files if you compile with -DGZIP. It requires that your Unix support the "popen" command. Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY options can make for faster parallel FFTs (in the PPPM solver) on some platforms. The -DPACK_ARRAY setting is the -default. +default. If you compile with -DLAMMPS_XDR, the build will include XDR +compatability files for doing particle dumps in XTC format. This is +only necessary if your platform does have its own XDR files available. +See the Restrictions section of the "dump"_dump.html command for +details. (8) The DEPFLAGS setting is how the C++ compiler creates a dependency file for each source file. This speeds re-compilation when source diff --git a/doc/dump.html b/doc/dump.html index 86cfe0dde1..d7d86a5d36 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -30,8 +30,7 @@
atom args = none
bond args = none
dcd args = none
- xtc args = precision (optional)
- precision = power-of-10 value from 10 to 1000000 (default = 1000)
+ xtc args = none
xyz args = none
custom args = list of atom attributes
possible attributes = tag, mol, type,
@@ -138,16 +137,31 @@ below.
The dcd style writes DCD files, a standard atomic trajectory format
used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
files are binary and thus may not be portable to different machines.
-The dump group must be all for the dcd style.
+The dump group must be all for 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.
The xtc style writes XTC files, a compressed trajectory format used
by the GROMACS molecular dynamics package, and described
here.
-The precision used in XTC files can be specified; for example, a value
-of 100 means that coordinates are stored to 1/100 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 dump group must be all for the xtc style.
+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
+dump group must be all for 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 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 xyz style writes XYZ files, which is a simple text-based
coordinate format that many codes can read.
@@ -310,12 +324,14 @@ some machines may not support the lo-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
makes it easy to exclude from a LAMMPS build for those machines.
-
-Some pair potentials do not allow the calculation of per-atom energy
-and stress via the epair, etotal, sxx, etc keywords. One of
-these are the granular pair potentials. However, for those
-potentials, the fix gran/diag command can be used
-instead.
+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,
+e.g. src/MAKE/Makefile.foo. This compatability 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.
Related commands:
diff --git a/doc/dump.txt b/doc/dump.txt
index ba0224c95f..26fb1485d5 100644
--- a/doc/dump.txt
+++ b/doc/dump.txt
@@ -21,8 +21,7 @@ args = list of arguments for a particular style :l
{atom} args = none
{bond} args = none
{dcd} args = none
- {xtc} args = precision (optional)
- precision = power-of-10 value from 10 to 1000000 (default = 1000)
+ {xtc} args = none
{xyz} args = none
{custom} args = list of atom attributes
possible attributes = tag, mol, type,
@@ -128,16 +127,31 @@ below.
The {dcd} style writes DCD files, a standard atomic trajectory format
used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
files are binary and thus may not be portable to different machines.
-The dump group must be {all} for the {dcd} style.
+The dump group must be {all} for 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.
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.
-The precision used in XTC files can be specified; for example, a value
-of 100 means that coordinates are stored to 1/100 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 dump group must be {all} for the {xtc} style.
+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
+dump group must be {all} for 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 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 {xyz} style writes XYZ files, which is a simple text-based
coordinate format that many codes can read.
@@ -300,12 +314,14 @@ some machines may not support the lo-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
makes it easy to exclude from a LAMMPS build for those machines.
-
-Some pair potentials do not allow the calculation of per-atom energy
-and stress via the {epair}, {etotal}, {sxx}, etc keywords. One of
-these are the granular pair potentials. However, for those
-potentials, the "fix gran/diag"_fix_gran_diag.html command can be used
-instead.
+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,
+e.g. src/MAKE/Makefile.foo. This compatability 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.
[Related commands:]
diff --git a/doc/dump_modify.html b/doc/dump_modify.html
index c5fc145d4c..2c183eb14d 100644
--- a/doc/dump_modify.html
+++ b/doc/dump_modify.html
@@ -19,14 +19,16 @@
format arg = C-style format string for one line of output
scale arg = yes or no
image arg = yes or no
flush arg = yes or no
+ unwrap arg = yes or no
every arg = N
N = dump every this many timesteps
+ precision arg = power-of-10 value from 10 to 1000000
region arg = region-ID or "none"
thresh args = attribute operation value
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
@@ -41,7 +43,8 @@
dump_modify 1 format "%d %d %20.15g %g %g" scale yes
dump_modify myDump image yes scale no flush yes
-dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
+dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
+dump_modify xtcdump precision 10000
Description:
@@ -76,10 +79,23 @@ the output in that file is current (no buffering by the OS), even if
LAMMPS halts before the simulation completes. Flushes cannot be
performed with dump style xtc.
+The unwrap option only applies to the dump dcd and xtc styles.
+If set to yes, coordinates will 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.
+
The every option changes the dump frequency originally specified by
the dump command to a new value which must be > 0. The
dump frequency cannot be changed for the dump dcd style.
+The precision option only applies to the dump xtc style. A
+specified value of N means that coordinates are stored to 1/N
+nanometer accuracy, e.g. for N = 1000, the coordinates are written to
+1/1000 nanometer accuracy.
+
The region keyword only applies to the dump custom style. If
specified, only atoms in the region will be written to the dump file.
Only one region can be applied as a filter (the last one specified).
@@ -109,6 +125,8 @@ whose energy is above some threshhold.
The option defaults are format = %d and %g for each integer or
floating point value, scale = yes, image = no, flush = yes (except for
-dump xtc style), region = none, and thresh = none.
+the dump xtc style), unwrap = no, every = whatever it was set to via
+the dump command, precision = 1000, region = none, and
+thresh = none.