Building LAMMPS can be non-trivial. You will likely need to edit a makefile, there are compiler options, additional libraries can be used -(MPI, FFT), etc. Please read this section carefully. If you are not -comfortable with makefiles, or building codes on a Unix platform, or -running an MPI job on your machine, please find a local expert to help -you. Many compiling, linking, and run problems that users are not -really LAMMPS issues - they are peculiar to the user's system, -compilers, libraries, etc. Such questions are better answered by a -local expert. +(MPI, FFT, JPEG), etc. Please read this section carefully. If you +are not comfortable with makefiles, or building codes on a Unix +platform, or running an MPI job on your machine, please find a local +expert to help you. Many compiling, linking, and run problems that +users are not really LAMMPS issues - they are peculiar to the user's +system, compilers, libraries, etc. Such questions are better answered +by a local expert.
If you have a build problem that you are convinced is a LAMMPS issue (e.g. the compiler complains about a line of LAMMPS source code), then @@ -196,18 +196,38 @@ which uses different rules that do not involve dependency files.
(3) The "system-specific settings" section has 4 parts.
(3.a) The LMP_INC variable is used to include options that turn on -system-dependent ifdefs within the LAMMPS code. +system-dependent ifdefs within the LAMMPS code. The settings +that are currently recogized are:
+The read_data and dump commands will read/write gzipped files if you compile with -DLAMMPS_GZIP. 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. -If you use -DLAMMPS_XDR, the build will include XDR compatibility +"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. See the +kspace_style command for info about PPPM. See +section (3.c) below for info about building LAMMPS with an FFT +library. +
+If you use -DLAMMPS_XDR, the build will include XDR compatibility 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 command for details.
+If you use -DLAMMPS_JPEG, the dump image command will be +able to write out JPEG image files. If not, it will only be able to +write out PPM image files. For JPEG files, you must also link LAMMPS +with a JPEG library. See section (3.d) below for more details on +this. +
(3.b) The 3 MPI variables are used to specify an MPI library to build LAMMPS with.
@@ -219,19 +239,20 @@ need to specify where the mpi.h file (MPI_INC) and the MPI library (MPI_PATH) is found and its name (MPI_LIB).If you are installing MPI yourself, we recommend Argonne's MPICH 1.2 -or 2.0 which can be downloaded from the Argonne MPI -site. LAM MPI should also work. If +or 2.0 or OpenMPI. MPICH can be downloaded from the Argonne MPI +site. OpenMPI can be downloaded the +OpenMPI site. LAM MPI should also work. If you are running on a big parallel platform, your system people or the vendor should have already installed a version of MPI, which will be -faster than MPICH or LAM, so find out how to build and link with it. -If you use MPICH or LAM, you will have to configure and build it for -your platform. The MPI configure script should have compiler options -to enable you to use the same compiler you are using for the LAMMPS -build, which can avoid problems that can arise when linking LAMMPS to -the MPI library. +faster than MPICH or OpenMPI or LAM, so find out how to build and link +with it. If you use MPICH or OpenMPI or LAM, you will have to +configure and build it for your platform. The MPI configure script +should have compiler options to enable you to use the same compiler +you are using for the LAMMPS build, which can avoid problems that can +arise when linking LAMMPS to the MPI library.
If you just want LAMMPS to run on a single processor, you can use the -STUBS library in place of MPI, since you don't need an MPI library +STUBS library in place of MPI, since you don't need a true MPI library installed on your system. See the Makefile.serial file for how to specify the 3 MPI variables. You will also need to build the STUBS library for your platform before making LAMMPS itself. From the STUBS @@ -259,7 +280,7 @@ should work on any platform. You can download it from 3.0.X. Building FFTW for your box should be as simple as ./configure; make. Whichever FFT library you have on your platform, you'll need to set the appropriate FFT_INC, FFT_PATH, and FFT_LIB variables in -Makefile.foo. +Makefile.foo, so the compiler and linker can find it.
If you examine src/fft3d.c and src.fft3d.h you'll see it's possible to add other vendor FFT libraries via #ifdef statements in the @@ -272,7 +293,18 @@ case you can set FFT_INC to -DFFT_NONE and leave the other 2 FFT variables blank. Or you can exclude the KSPACE package when you build LAMMPS (see below).
-(3.d) The several SYSLIB and SYSPATH variables can be ignored unless +
(3.d) The 3 JPG variables are used to specify a JPEG library which +LAMMPS uses when writing a JPEG file via the dump +image command. These can be left blank if you are +not using the -DLAMMPS_JPEG switch discussed above in section (3.a). +
+A standard JPEG library usually goes by the name libjpeg.a and has an +associated header file jpeglib.h. Whichever JPEG library you have on +your platform, you'll need to set the appropriate JPG_INC, JPG_PATH, +and JPG_LIB variables in Makefile.foo so that the compiler and linker +can find it. +
+(3.e) The several SYSLIB and SYSPATH variables can be ignored unless you are building LAMMPS with one or more of the LAMMPS packages that require these extra system libraries. The names of these packages are the prefixes on the SYSLIB and SYSPATH variables. See the section diff --git a/doc/Section_start.txt b/doc/Section_start.txt index 10a5a3ba84..4b4d96693f 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -78,13 +78,13 @@ This section has the following sub-sections: Building LAMMPS can be non-trivial. You will likely need to edit a makefile, there are compiler options, additional libraries can be used -(MPI, FFT), etc. Please read this section carefully. If you are not -comfortable with makefiles, or building codes on a Unix platform, or -running an MPI job on your machine, please find a local expert to help -you. Many compiling, linking, and run problems that users are not -really LAMMPS issues - they are peculiar to the user's system, -compilers, libraries, etc. Such questions are better answered by a -local expert. +(MPI, FFT, JPEG), etc. Please read this section carefully. If you +are not comfortable with makefiles, or building codes on a Unix +platform, or running an MPI job on your machine, please find a local +expert to help you. Many compiling, linking, and run problems that +users are not really LAMMPS issues - they are peculiar to the user's +system, compilers, libraries, etc. Such questions are better answered +by a local expert. If you have a build problem that you are convinced is a LAMMPS issue (e.g. the compiler complains about a line of LAMMPS source code), then @@ -191,18 +191,38 @@ which uses different rules that do not involve dependency files. (3) The "system-specific settings" section has 4 parts. (3.a) The LMP_INC variable is used to include options that turn on -system-dependent ifdefs within the LAMMPS code. +system-dependent ifdefs within the LAMMPS code. The settings +that are currently recogized are: + +-DLAMMPS_GZIP +-DPACK_ARRAY +-DPACK_POINTER +-DPACK_MEMCPY +-DLAMMPS_XDR +-DLAMMPS_JPEG :ul The read_data and dump commands will read/write gzipped files if you compile with -DLAMMPS_GZIP. 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. +"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. See the +"kspace_style"_kspace_style.html command for info about PPPM. See +section (3.c) below for info about building LAMMPS with an FFT +library. + If you use -DLAMMPS_XDR, the build will include XDR compatibility 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. +If you use -DLAMMPS_JPEG, the "dump image"_dump.html command will be +able to write out JPEG image files. If not, it will only be able to +write out PPM image files. For JPEG files, you must also link LAMMPS +with a JPEG library. See section (3.d) below for more details on +this. + (3.b) The 3 MPI variables are used to specify an MPI library to build LAMMPS with. @@ -214,19 +234,20 @@ need to specify where the mpi.h file (MPI_INC) and the MPI library (MPI_PATH) is found and its name (MPI_LIB). If you are installing MPI yourself, we recommend Argonne's MPICH 1.2 -or 2.0 which can be downloaded from the "Argonne MPI -site"_http://www-unix.mcs.anl.gov/mpi. LAM MPI should also work. If +or 2.0 or OpenMPI. MPICH can be downloaded from the "Argonne MPI +site"_http://www-unix.mcs.anl.gov/mpi. OpenMPI can be downloaded the +"OpenMPI site"_http://www.open-mpi.org. LAM MPI should also work. If you are running on a big parallel platform, your system people or the vendor should have already installed a version of MPI, which will be -faster than MPICH or LAM, so find out how to build and link with it. -If you use MPICH or LAM, you will have to configure and build it for -your platform. The MPI configure script should have compiler options -to enable you to use the same compiler you are using for the LAMMPS -build, which can avoid problems that can arise when linking LAMMPS to -the MPI library. +faster than MPICH or OpenMPI or LAM, so find out how to build and link +with it. If you use MPICH or OpenMPI or LAM, you will have to +configure and build it for your platform. The MPI configure script +should have compiler options to enable you to use the same compiler +you are using for the LAMMPS build, which can avoid problems that can +arise when linking LAMMPS to the MPI library. If you just want LAMMPS to run on a single processor, you can use the -STUBS library in place of MPI, since you don't need an MPI library +STUBS library in place of MPI, since you don't need a true MPI library installed on your system. See the Makefile.serial file for how to specify the 3 MPI variables. You will also need to build the STUBS library for your platform before making LAMMPS itself. From the STUBS @@ -254,7 +275,7 @@ should work on any platform. You can download it from 3.0.X. Building FFTW for your box should be as simple as ./configure; make. Whichever FFT library you have on your platform, you'll need to set the appropriate FFT_INC, FFT_PATH, and FFT_LIB variables in -Makefile.foo. +Makefile.foo, so the compiler and linker can find it. If you examine src/fft3d.c and src.fft3d.h you'll see it's possible to add other vendor FFT libraries via #ifdef statements in the @@ -267,7 +288,18 @@ case you can set FFT_INC to -DFFT_NONE and leave the other 2 FFT variables blank. Or you can exclude the KSPACE package when you build LAMMPS (see below). -(3.d) The several SYSLIB and SYSPATH variables can be ignored unless +(3.d) The 3 JPG variables are used to specify a JPEG library which +LAMMPS uses when writing a JPEG file via the "dump +image"_dump_image.html command. These can be left blank if you are +not using the -DLAMMPS_JPEG switch discussed above in section (3.a). + +A standard JPEG library usually goes by the name libjpeg.a and has an +associated header file jpeglib.h. Whichever JPEG library you have on +your platform, you'll need to set the appropriate JPG_INC, JPG_PATH, +and JPG_LIB variables in Makefile.foo so that the compiler and linker +can find it. + +(3.e) The several SYSLIB and SYSPATH variables can be ignored unless you are building LAMMPS with one or more of the LAMMPS packages that require these extra system libraries. The names of these packages are the prefixes on the SYSLIB and SYSPATH variables. See the "section diff --git a/doc/compute_pair_local.html b/doc/compute_pair_local.html index 0fe54e113d..f6bea11cea 100644 --- a/doc/compute_pair_local.html +++ b/doc/compute_pair_local.html @@ -62,6 +62,16 @@ property/local command can be combined with data from this command and output by the dump local command in a consistent way.
+IMPORTANT NOTE: For pairs, if two atoms I,J are involved in 1-2, 1-3, +1-4 interactions within the molecular topology, their pairwise +interaction may be turned off, and thus they may not appear in the +neighbor list, and will not be part of the local data created by this +command. More specifically, this may be true of I,J pairs with a +weighting factor of 0.0; pairs with a non-zero weighting factor are +included. The weighting factors for 1-2, 1-3, and 1-4 pairwise +interactions are set by the special_bonds +command. +
Output info:
This compute calculates a local vector or local array depending on the diff --git a/doc/compute_pair_local.txt b/doc/compute_pair_local.txt index 9caefb5e18..0659e80821 100644 --- a/doc/compute_pair_local.txt +++ b/doc/compute_pair_local.txt @@ -54,6 +54,16 @@ property/local"_compute_property_local.html command can be combined with data from this command and output by the "dump local"_dump.html command in a consistent way. +IMPORTANT NOTE: For pairs, if two atoms I,J are involved in 1-2, 1-3, +1-4 interactions within the molecular topology, their pairwise +interaction may be turned off, and thus they may not appear in the +neighbor list, and will not be part of the local data created by this +command. More specifically, this may be true of I,J pairs with a +weighting factor of 0.0; pairs with a non-zero weighting factor are +included. The weighting factors for 1-2, 1-3, and 1-4 pairwise +interactions are set by the "special_bonds"_special_bonds.html +command. + [Output info:] This compute calculates a local vector or local array depending on the diff --git a/doc/compute_property_local.html b/doc/compute_property_local.html index 9583f4749d..546ff6ff54 100644 --- a/doc/compute_property_local.html +++ b/doc/compute_property_local.html @@ -95,9 +95,9 @@ by the pair_style command.
IMPORTANT NOTE: For pairs, if two atoms I,J are involved in 1-2, 1-3, 1-4 interactions within the molecular topology, their pairwise -interaction may be turned off, and thus they will not appear in the +interaction may be turned off, and thus they may not appear in the neighbor list, and will not be part of the local data created by this -command. More specifically, this is true of I,J pairs with a +command. More specifically, this may be true of I,J pairs with a weighting factor of 0.0; pairs with a non-zero weighting factor are included. The weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set by the special_bonds diff --git a/doc/compute_property_local.txt b/doc/compute_property_local.txt index 1baaedd069..1f3726b43b 100644 --- a/doc/compute_property_local.txt +++ b/doc/compute_property_local.txt @@ -88,9 +88,9 @@ by the "pair_style"_pair_style.html command. IMPORTANT NOTE: For pairs, if two atoms I,J are involved in 1-2, 1-3, 1-4 interactions within the molecular topology, their pairwise -interaction may be turned off, and thus they will not appear in the +interaction may be turned off, and thus they may not appear in the neighbor list, and will not be part of the local data created by this -command. More specifically, this is true of I,J pairs with a +command. More specifically, this may be true of I,J pairs with a weighting factor of 0.0; pairs with a non-zero weighting factor are included. The weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set by the "special_bonds"_special_bonds.html diff --git a/doc/compute_rdf.html b/doc/compute_rdf.html index a6ded207ca..dd93bfd8f2 100644 --- a/doc/compute_rdf.html +++ b/doc/compute_rdf.html @@ -72,19 +72,8 @@ a specific histogram if the following criteria are met:
IMPORTANT NOTE: The last point is relevant for molecular systems with -bonds, because if two atoms I,J are involved in 1-2, 1-3, 1-4 -interactions within the molecular topology, their pairwise interaction -may be turned off, and thus they will not appear in the neighbor list, -and will not contribute to g(r). More specifically, this is true of -I,J pairs with a weighting factor of 0.0; pairs with a non-zero -weighting factor are included. The weighting factors for 1-2, 1-3, -and 1-4 pairwise interactions are set by the -special_bonds command. -
It is OK if a particular pairwise distance is included in more than one individual histogram, due to the way the itypeN and jtypeN arguments are specified. diff --git a/doc/compute_rdf.txt b/doc/compute_rdf.txt index 595087af04..a4ddf137d7 100644 --- a/doc/compute_rdf.txt +++ b/doc/compute_rdf.txt @@ -69,18 +69,7 @@ a specific histogram if the following criteria are met: atoms I,J are both in the specified compute group the distance between atoms I,J is less than the maximum force cutoff the type of the I atom matches itypeN (one or a range of types) -the type of the J atom matches jtypeN (one or a range of types) -the I,J interaction is included in the neighbor list :ul - -IMPORTANT NOTE: The last point is relevant for molecular systems with -bonds, because if two atoms I,J are involved in 1-2, 1-3, 1-4 -interactions within the molecular topology, their pairwise interaction -may be turned off, and thus they will not appear in the neighbor list, -and will not contribute to g(r). More specifically, this is true of -I,J pairs with a weighting factor of 0.0; pairs with a non-zero -weighting factor are included. The weighting factors for 1-2, 1-3, -and 1-4 pairwise interactions are set by the -"special_bonds"_special_bonds.html command. +the type of the J atom matches jtypeN (one or a range of types) :ul It is OK if a particular pairwise distance is included in more than one individual histogram, due to the way the {itypeN} and {jtypeN} diff --git a/doc/dump.html b/doc/dump.html index fad0888e9a..0dd5e729d9 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -11,6 +11,8 @@
Syntax:
dump ID group-ID style N file args @@ -19,7 +21,7 @@
image args = discussed on dump image doc page +
local args = list of local attributes
possible attributes = index, c_ID, c_ID[N], f_ID, f_ID[N]
index = enumeration of local values
@@ -95,13 +99,19 @@ dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce
Description:
Dump a snapshot of atom quantities to one or more files every N
-timesteps in one of several styles. As described below, the filename
-determines the kind of output (text or binary or gzipped, one big file
-or one per timestep, one big file or one per processor). Only
-information for atoms in the specified group is dumped. The
-dump_modify command can also alter what atoms are
-included. Not all styles support all these options; see details
-below.
+timesteps in one of several styles. The image style is the
+exception; it creates a JPG or PPM image file of the atom
+configuration every N timesteps, as discussed on the dump
+image doc page.
+
+Only information for atoms in the specified group is dumped. The
+dump_modify thresh and region commands can also
+alter what atoms are included. Not all styles support all these
+options; see details below.
+
+As described below, the filename determines the kind of output (text
+or binary or gzipped, one big file or one per timestep, one big file
+or one per processor).
IMPORTANT NOTE: Because periodic boundary conditions are enforced only
on timesteps when neighbor lists are rebuilt, the coordinates of an
@@ -142,20 +152,25 @@ self-describing in the following sense.
The dimensions of the simulation box are included in each snapshot.
For an orthogonal simulation box this information is is formatted as:
-ITEM: BOX BOUNDS
+ITEM: BOX BOUNDS xx yy zz
xlo xhi
ylo yhi
zlo zhi
where xlo,xhi are the maximum extents of the simulation box in the
-x-dimension, and similarly for y and z.
+x-dimension, and similarly for y and z. The "xx yy zz" represent 6
+characters that encode the style of boundary for each of the 6
+simulation box boundaries (xlo,xhi and ylo,yhi and zlo,zhi). Each
+flag is either p = periodic, f = fixed, s = shrink wrap, or m = shrink
+wrapped with a minimum value. See the boundary
+command for details.
For triclinic simulation boxes (non-orthogonal), an orthogonal
bounding box which encloses the triclinic simulation box is output,
along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
formatted as follows:
-ITEM: BOX BOUNDS xy xz yz
+ITEM: BOX BOUNDS xx yy zz xy xz yz
xlo_bound xhi_bound xy
ylo_bound yhi_bound xz
zlo_bound zhi_bound yz
@@ -281,7 +296,10 @@ character appears in the filename, then one file per snapshot is
written and the "*" character is replaced with the timestep value.
For example, tmp.dump.* becomes tmp.dump.0, tmp.dump.10000,
tmp.dump.20000, etc. This option is not available for the dcd and
-xtc styles.
+xtc styles. Note that the dump_modify pad
+command can be used to insure all timestep numbers are the same length
+(e.g. 00010), which can make it easier to read a series of dump files
+in order by some post-processing tools.
If a "%" character appears in the filename, then one file is written
for each processor and the "%" character is replaced with the
@@ -490,8 +508,12 @@ should also work on IBM BG/P, and Windows XP/Vista/7 machines.
Related commands:
-dump image, dump_modify,
+undump
-Default: none
+
Default:
+
+The defaults for the image style are listed on the dump
+image doc page.