Merge pull request #1928 from akohlmey/collected-small-fixes (f1cc6c6e) · Commits · 郑智淋 / lammps

doc/src/kspace_style.rst

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	@@ -406,8 +406,8 @@ interactions. Vacuum boundary conditions are not currently supported.

	The ewald/disp\ , ewald\ , pppm\ , and msm styles support		The ewald/disp\ , ewald\ , pppm\ , and msm styles support
	non-orthogonal (triclinic symmetry) simulation boxes. However,		non-orthogonal (triclinic symmetry) simulation boxes. However,
	triclinic simulation cells may not yet be supported by suffix versions		triclinic simulation cells may not yet be supported by all suffix
	of these styles.		versions of these styles.

	All of the kspace styles are part of the KSPACE package. They are		All of the kspace styles are part of the KSPACE package. They are
	only enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.		only enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.

doc/src/server_md.txt

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	"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

	:link(lws,http://lammps.sandia.gov)
	:link(ld,Manual.html)
	:link(lc,Commands_all.html)

	:line

	server md command :h3

	[Syntax:]

	server md :pre

	md = the protocol argument to the "server"_server.html command

	[Examples:]

	server md :pre

	[Description:]

	This command starts LAMMPS running in "server" mode, where it will
	expect messages from a separate "client" code that match the {md}
	protocol for format and content explained below. For each message
	LAMMPS receives it will send a message back to the client.

	The "Howto client/server"_Howto_client_server.html doc page gives an
	overview of client/server coupling of LAMMPS with another code where
	one code is the "client" and sends request messages to a "server"
	code. The server responds to each request with a reply message. This
	enables the two codes to work in tandem to perform a simulation.

	When this command is invoked, LAMMPS will run in server mode in an
	endless loop, waiting for messages from the client code. The client
	signals when it is done sending messages to LAMMPS, at which point the
	loop will exit, and the remainder of the LAMMPS script will be
	processed.

	The "server"_server.html doc page gives other options for using LAMMPS
	in server mode. See an example of how this command is used in
	examples/message/in.message.server.

	:line

	When using this command, LAMMPS (as the server code) receives the
	current coordinates of all particles from the client code each
	timestep, computes their interaction, and returns the energy, forces,
	and pressure for the interacting particles to the client code, so it
	can complete the timestep. This command could also be used with a
	client code that performs energy minimization, using the server to
	compute forces and energy each iteration of its minimizer.

	When using the "fix client/md"_fix_client_md.html command, LAMMPS (as
	the client code) does the timestepping and receives needed energy,
	forces, and pressure values from the server code.

	The format and content of the exchanged messages are explained here in
	a conceptual sense. Python-style pseudo code for the library calls to
	the CSlib is shown, which performs the actual message exchange between
	the two codes. See the "CSlib website"_http://cslib.sandia.gov doc
	pages for more details on the actual library syntax. The "cs" object
	in this pseudo code is a pointer to an instance of the CSlib.

	See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp
	files for details on how LAMMPS uses these messages. See the
	examples/COUPLE/lammps_vasp/vasp_wrap.py or
	examples/COUPLE/lammps_nwchem/nwchem_wrap.py files for examples of how
	a quantum code (VASP or NWChem) can use these messages.

	The following pseudo-code uses these values, defined as enums.

	Define:

	SETUP=1, STEP=2
	DIM=1, PERIODICITY=2, ORIGIN=3, BOX=4, NATOMS=5, NTYPES=6, TYPES=7, COORDS=8, UNITS-9, CHARGE=10
	FORCES=1, ENERGY=2, PRESSURE=3, ERROR=4 :pre

	[Client sends 2 kinds of messages]:

	# required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS
	# optional fields: UNITS, CHARGE :pre

	cs->send(SETUP,nfields) # msgID with nfields :pre

	cs->pack_int(DIM,dim) # dimension (2,3) of simulation
	cs->pack(PERIODICITY,3,xyz) # periodicity flags in 3 dims
	cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box
	cs->pack(BOX,9,box) # 3 edge vectors of simulation box
	cs->pack_int(NATOMS,natoms) # total number of atoms
	cs->pack_int(NTYPES,ntypes) # number of atom types
	cs->pack(TYPES,natoms,type) # vector of per-atom types
	cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords
	cs->pack_string(UNITS,units) # units = "lj", "real", "metal", etc
	cs->pack(CHARGE,natoms,q) # vector of per-atom charge :pre

	# required fields: COORDS
	# optional fields: ORIGIN, BOX :pre

	cs->send(STEP,nfields) # msgID with nfields :pre

	cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords
	cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box
	cs->pack(BOX,9,box) # 3 edge vectors of simulation box :pre

	[Server replies to either kind of message]:

	# required fields: FORCES, ENERGY, PRESSURE
	# optional fields: ERROR :pre

	cs->send(msgID,nfields) # msgID with nfields
	cs->pack(FORCES,3*Natoms,f) # vector of 3N forces on atoms
	cs->pack(ENERGY,1,poteng) # total potential energy of system
	cs->pack(PRESSURE,6,press) # global pressure tensor (6-vector)
	cs->pack_int(ERROR,flag) # server had an error (e.g. DFT non-convergence) :pre

	:line

	The units for various quantities that are sent and received iva
	messages are defined for atomic-scale simulations in the table below.
	The client and server codes (including LAMMPS) can use internal units
	different than these (e.g. "real units"_units.html in LAMMPS), so long
	as they convert to these units for messaging.

	COORDS, ORIGIN, BOX = Angstroms
	CHARGE = multiple of electron charge (1.0 is a proton)
	ENERGY = eV
	FORCES = eV/Angstrom
	PRESSURE = bars :ul

	Note that these are "metal units"_units.html in LAMMPS.

	If you wish to run LAMMPS in another its non-atomic units, e.g. "lj
	units"_units.html, then the client and server should exchange a UNITS
	message as indicated above, and both the client and server should
	agree on the units for the data they exchange.

	:line

	[Restrictions:]

	This command is part of the MESSAGE package. It is only enabled if
	LAMMPS was built with that package. See the "Build
	package"_Build_package.html doc page for more info.

	[Related commands:]

	"message"_message.html, "fix client/md"_fix_client_md.html

	[Default:] none

src/KIM/kim_init.h

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	@@ -69,7 +69,7 @@ CommandStyle(kim_init,KimInit)
	#include <string>		#include <string>

	// Forward declaration.		// Forward declaration.
	class KIM_Model;		typedef struct KIM_Model KIM_Model;

	namespace LAMMPS_NS {		namespace LAMMPS_NS {

src/MESSAGE/fix_client_md.cpp

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	@@ -45,7 +45,7 @@ FixClientMD::FixClientMD(LAMMPS lmp, int narg, char *arg) :
	if (!atom->map_style) error->all(FLERR,"Fix client/md requires atom map");		if (!atom->map_style) error->all(FLERR,"Fix client/md requires atom map");

	if (sizeof(tagint) != 4)		if (sizeof(tagint) != 4)
	error->all(FLERR,"Fix client/md requires 4-byte atom IDs");		error->all(FLERR,"Fix client/md only supports 32-bit atom IDs");

	if (strcmp(update->unit_style,"real") == 0) units = REAL;		if (strcmp(update->unit_style,"real") == 0) units = REAL;
	else if (strcmp(update->unit_style,"metal") == 0) units = METAL;		else if (strcmp(update->unit_style,"metal") == 0) units = METAL;

src/MESSAGE/server_mc.cpp

+6 −7

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	@@ -13,6 +13,7 @@

	#include "server_mc.h"		#include "server_mc.h"
	#include "atom.h"		#include "atom.h"
			#include "domain.h"
	#include "update.h"		#include "update.h"
	#include "integrate.h"		#include "integrate.h"
	#include "input.h"		#include "input.h"
	@@ -43,17 +44,17 @@ void ServerMC::loop()

	CSlib cs = (CSlib ) lmp->cslib;		CSlib cs = (CSlib ) lmp->cslib;

	// require atom map		if (domain->box_exist == 0)
			error->all(FLERR,"Server command before simulation box is defined");

	if (!atom->map_style) error->all(FLERR,"Server mode requires atom map");		if (!atom->map_style) error->all(FLERR,"Server mc requires atom map");
			if (atom->tag_enable == 0) error->all(FLERR,"Server mc requires atom IDs");
			if (sizeof(tagint) != 4) error->all(FLERR,"Server mc requires 32-bit atom IDs");

	// initialize LAMMPS for dynamics		// initialize LAMMPS for dynamics

	input->one("run 0");		input->one("run 0");

	//update->whichflag = 1;
	//lmp->init();

	// loop on messages		// loop on messages
	// receive a message, process it, send return message if necessary		// receive a message, process it, send return message if necessary

	@@ -123,8 +124,6 @@ void ServerMC::loop()

	int nsteps = cs->unpack_int(1);		int nsteps = cs->unpack_int(1);

	//input->one("run 100");

	update->nsteps = nsteps;		update->nsteps = nsteps;
	update->firststep = update->ntimestep;		update->firststep = update->ntimestep;
	update->laststep = update->ntimestep + nsteps;		update->laststep = update->ntimestep + nsteps;

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