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forgot pair table change

This commit is contained in:
Steve Plimpton 2016-10-19 10:47:07 -06:00
parent 3d254780de
commit 9954d5d346
9 changed files with 106 additions and 56 deletions
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4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="18 Oct 2016 version">
<META NAME="docnumber" CONTENT="19 Oct 2016 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<H1></H1>
LAMMPS Documentation :c,h3
18 Oct 2016 version :c,h4
19 Oct 2016 version :c,h4
Version info: :h4

2
doc/src/Section_commands.txt
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@ -528,6 +528,8 @@ These are additional commands in USER packages, which can be used if
package"_Section_start.html#start_3.
"dump custom/vtk"_dump_custom_vtk.html,
"dump nc"_dump_nc.html,
"dump nc/mpiio"_dump_nc.html,
"group2ndx"_group2ndx.html,
"ndx2group"_group2ndx.html :tb(c=3,ea=c)

91
doc/src/Section_howto.txt
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@ -1854,13 +1854,19 @@ internal LAMMPS operations. Note that LAMMPS classes are defined
within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
application.
Library.cpp contains these 5 basic functions:
Library.cpp contains these functions for creating and destroying an
instance of LAMMPS and sending it commands to execute. See the
documentation in the src/library.cpp file for details:
void lammps_open(int, char **, MPI_Comm, void **)
void lammps_open_no_mpi(int, char **, void **)
void lammps_close(void *)
int lammps_version(void *)
void lammps_file(void *, char *)
char *lammps_command(void *, char *) :pre
char *lammps_command(void *, char *)
char *lammps_commands_list(void *, int, char **)
char *lammps_commands_concatenated(void *, char *)
void lammps_free(void *) :pre
The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were "command-line
@ -1880,6 +1886,10 @@ half to the other code and run both codes simultaneously before
syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.
The lammps_open_no_mpi() function is similar except that no MPI
communicator is passed from the caller. Instead, MPI_COMM_WORLD is
used to instantiate LAMMPS, and MPI is initialzed if necessary.
The lammps_close() function is used to shut down an instance of LAMMPS
and free all its memory.
@ -1891,16 +1901,33 @@ changes to the LAMMPS command syntax between versions. The returned
LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
20150902) that grows with every new LAMMPS version.
The lammps_file() and lammps_command() functions are used to pass a
file or string to LAMMPS as if it were an input script or single
command in an input script. Thus the calling code can read or
generate a series of LAMMPS commands one line at a time and pass it
thru the library interface to setup a problem and then run it,
interleaving the lammps_command() calls with other calls to extract
information from LAMMPS, perform its own operations, or call another
The lammps_file(), lammps_command(), lammps_commands_list(),
lammps_commands_concatenated() functions are used to pass one or more
commands to LAMMPS to execute as if they were coming from an input
script.
The lammps_file() function passes the filename of an input script.
The lammps_command() function passes a single command as a string.
The lammps_commands_multiple() function passes multiple commands in a
char** list. The lammps_commands_concatentaed() function passes
multiple commands concatenated into one long string, separated by
newline characters. A single command can be spread across multiple
lines, if the last printable character of all but the last line is
"&", the same as if the lines appeared in an input script.
Via these library functions, the calling code can read or generate a
series of LAMMPS commands one or multiple at a time and pass it thru
the library interface to setup a problem and then run it, interleaving
the command function calls with operations performed within the
faller, calls to extract information from LAMMPS, or calls to another
code's library.
Other useful functions are also included in library.cpp. For example:
The lammps_free() is a clean-up function to free memory that the library
allocated previously.
Library.cpp also contains these functions for extracting information
from LAMMPS and setting value within LAMMPS. Again, see the
documentation in the src/library.cpp file for details:
void *lammps_extract_global(void *, char *)
void *lammps_extract_atom(void *, char *)
@ -1908,27 +1935,37 @@ void *lammps_extract_compute(void *, char *, int, int)
void *lammps_extract_fix(void *, char *, int, int, int, int)
void *lammps_extract_variable(void *, char *, char *)
int lammps_set_variable(void *, char *, char *)
double lammps_get_thermo(void *, char *)
int lammps_get_natoms(void *)
void lammps_get_coords(void *, double *)
void lammps_put_coords(void *, double *) :pre
void lammps_gather_atoms(void *, double *)
void lammps_scatter_atoms(void *, double *) :pre
These can extract various global or per-atom quantities from LAMMPS as
well as values calculated by a compute, fix, or variable. The
"set_variable" function can set an existing string-style variable to a
new value, so that subsequent LAMMPS commands can access the variable.
The "get" and "put" operations can retrieve and reset atom
coordinates. See the library.cpp file and its associated header file
library.h for details.
These functions can extract various global or per-atom quantities from
LAMMPS as well as values calculated by a compute, fix, or variable.
The lammps_set_variable() function can set an existing string-style variable
to a new value, so that subsequent LAMMPS commands can access the
variable. The lammps_get_thermo() function returns the current
value of a thermo keyword.
The key idea of the library interface is that you can write any
functions you wish to define how your code talks to LAMMPS and add
them to src/library.cpp and src/library.h, as well as to the "Python
The lammps_get_natoms() function returns the total number of atoms in
the system and can be used by the caller to allocate space for the
lammps_gather_atoms() and lammps_scatter_atoms() functions. The
gather function collects atom info of the requested type (atom coords,
types, forces, etc) from all procsesors, orders them by atom ID, and
returns a full list to each calling processor. The scatter function
does the inverse. It distributes the same kinds of values,
passed by the caller, to each atom owned by individual processors.
The examples/COUPLE and python directories have example C++ and C and
Python codes which show how a driver code can link to LAMMPS as a
library, run LAMMPS on a subset of processors, grab data from LAMMPS,
change it, and put it back into LAMMPS.
NOTE: You can write your own additional functions as needed to define
how your code talks to LAMMPS and add them to src/library.cpp and
src/library.h, as well as to the "Python
interface"_Section_python.html. The routines you add can access or
change any LAMMPS data you wish. The examples/COUPLE and python
directories have example C++ and C and Python codes which show how a
driver code can link to LAMMPS as a library, run LAMMPS on a subset of
processors, grab data from LAMMPS, change it, and put it back into
LAMMPS.
change any LAMMPS data you wish.
:line

15
doc/src/Section_python.txt
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@ -534,10 +534,11 @@ from lammps import lammps :pre
These are the methods defined by the lammps module. If you look at
the files src/library.cpp and src/library.h you will see that they
correspond one-to-one with calls you can make to the LAMMPS library
from a C++ or C or Fortran program.
from a C++ or C or Fortran program, and which are described in
"Section 6.19"_Section_howto.html#howto_19 of the manual.
lmp = lammps() # create a LAMMPS object using the default liblammps.so library
4 optional args are allowed: name, cmdargs, ptr, comm
# 4 optional args are allowed: name, cmdargs, ptr, comm
lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
lmp = lammps(name="g++") # create a LAMMPS object using the liblammps_g++.so library
@ -549,6 +550,7 @@ version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 20
lmp.file(file) # run an entire input script, file = "in.lj"
lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" :pre
lmp.commands_list(cmdlist) # invoke commands in cmdlist
xlo = lmp.extract_global(name,type) # extract a global quantity
# name = "boxxlo", "nlocal", etc
@ -580,6 +582,8 @@ var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable
# 1 = atom-style variable :pre
flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful
value = lmp.get_thermo(name) # return current value of a thermo keyword
natoms = lmp.get_natoms() # total # of atoms as int
data = lmp.gather_atoms(name,type,count) # return atom attribute of all atoms gathered into data, ordered by atom ID
# name = "x", "charge", "type", etc
@ -599,9 +603,10 @@ create an instance of LAMMPS, wrapped in a Python class by the lammps
Python module, and return an instance of the Python class as lmp. It
is used to make all subequent calls to the LAMMPS library.
Additional arguments can be used to tell Python the name of the shared
library to load or to pass arguments to the LAMMPS instance, the same
as if LAMMPS were launched from a command-line prompt.
Additional arguments to lammps() can be used to tell Python the name
of the shared library to load or to pass arguments to the LAMMPS
instance, the same as if LAMMPS were launched from a command-line
prompt.
If the ptr argument is set like this:

5
doc/src/dump.txt
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@ -12,6 +12,7 @@ dump command :h3
"dump image"_dump_image.html command :h3
"dump movie"_dump_image.html command :h3
"dump molfile"_dump_molfile.html command :h3
"dump nc"_dump_nc.html command :h3
[Syntax:]
@ -43,7 +44,9 @@ args = list of arguments for a particular style :l
{movie} args = discussed on "dump image"_dump_image.html doc page :pre
{molfile} args = discussed on "dump molfile"_dump_molfile.html doc page :pre
{molfile} args = discussed on "dump molfile"_dump_molfile.html doc page
{nc} args = discussed on "dump nc"_dump_nc.html doc page :pre
{local} args = list of local attributes
possible attributes = index, c_ID, c_ID\[I\], f_ID, f_ID\[I\]

38
doc/src/dump_nc.txt
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@ -31,30 +31,32 @@ dump 1 all nc/mpiio 1000 traj.nc id type x y z :pre
[Description:]
Dump a snapshot of atom coordinates every N timesteps in Amber-style
NetCDF file format. NetCDF files are binary, portable and self-describing.
This dump style will write only one file on the root node. The dump
style {nc} uses the "standard NetCDF library"_netcdf-home all data is
collected on one processor and then written to the dump file. Dump style
{nc/mpiio} used the "parallel NetCDF library"_pnetcdf-home and MPI-IO;
it has better performance on a larger number of processors. Note that
'nc' outputs all atoms sorted by atom tag while 'nc/mpiio' outputs in
order of the MPI rank.
NetCDF file format. NetCDF files are binary, portable and
self-describing. This dump style will write only one file on the root
node. The dump style {nc} uses the "standard NetCDF
library"_netcdf-home all data is collected on one processor and then
written to the dump file. Dump style {nc/mpiio} used the "parallel
NetCDF library"_pnetcdf-home and MPI-IO; it has better performance on
a larger number of processors. Note that 'nc' outputs all atoms sorted
by atom tag while 'nc/mpiio' outputs in order of the MPI rank.
In addition to per-atom data, also global (i.e. not per atom, but per frame)
quantities can be included in the dump file. This can be variables, output
from computes or fixes data prefixed with v_, c_ and f_, respectively.
These properties are included via "dump_modify"_dump_modify.html {global}.
In addition to per-atom data, also global (i.e. not per atom, but per
frame) quantities can be included in the dump file. This can be
variables, output from computes or fixes data prefixed with v_, c_ and
f_, respectively. These properties are included via
"dump_modify"_dump_modify.html {global}.
:link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
:link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)
:line
[Restrictions:]
The {nc} and {nc/mpiio} dump styles are part of the USER-NC-DUMP package.
It is only enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
:link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
:link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)
The {nc} and {nc/mpiio} dump styles are part of the USER-NC-DUMP
package. It is only enabled if LAMMPS was built with that
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info.
:line

1
doc/src/fix.txt
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@ -190,6 +190,7 @@ of "this page"_Section_commands.html#cmd_5.
"gcmc"_fix_gcmc.html - grand canonical insertions/deletions
"gld"_fix_gcmc.html - generalized Langevin dynamics integrator
"gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
"halt"_fix_halt.html - terminate a dynamics run or minimization
"heat"_fix_heat.html - add/subtract momentum-conserving heat
"indent"_fix_indent.html - impose force due to an indenter
"langevin"_fix_langevin.html - Langevin temperature control

4
src/pair_table.cpp
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@ -554,7 +554,7 @@ void PairTable::spline_table(Table *tb)
/* ----------------------------------------------------------------------
extract attributes from parameter line in table section
format of line: N value R/RSQ/BITMAP lo hi FP fplo fphi
format of line: N value R/RSQ/BITMAP lo hi FPRIME fplo fphi
N is required, other params are optional
------------------------------------------------------------------------- */
@ -578,7 +578,7 @@ void PairTable::param_extract(Table *tb, char *line)
tb->rlo = atof(word);
word = strtok(NULL," \t\n\r\f");
tb->rhi = atof(word);
} else if (strcmp(word,"FP") == 0) {
} else if (strcmp(word,"FPRIME") == 0) {
tb->fpflag = 1;
word = strtok(NULL," \t\n\r\f");
tb->fplo = atof(word);

2
src/version.h
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@ -1 +1 @@
#define LAMMPS_VERSION "18 Oct 2016"
#define LAMMPS_VERSION "19 Oct 2016"