docs for MD protocol enhancements (d8b087ae) · Commits · 郑智淋 / lammps

doc/src/server_mc.txt

+9 −9

Original line number	Diff line number	Diff line
		@@ -71,26 +71,26 @@ cs->send(NATOMS,0) # msgID = 1 with no fields :pre
		cs->send(EINIT,0) # msgID = 2 with no fields :pre

		cs->send(DISPLACE,2) # msgID = 3 with 2 fields
		cs->pack(1,1,ID) # 1st field = ID of atom to displace
		cs->pack_int(1,ID) # 1st field = ID of atom to displace
		cs->pack(2,3,xnew) # 2nd field = new xyz coords of displaced atom :pre

		cs->send(ACCEPT,1) # msgID = 4 with 1 field
		cs->pack(1,1,flag) # 1st field = accept/reject flag :pre
		cs->pack_int(1,flag) # 1st field = accept/reject flag :pre

		cs->send(RUN,1) # msgID = 5 with 1 field
		cs->pack(1,1,nsteps) # 1st field = # of timesteps to run MD :pre
		cs->pack_int(1,nsteps) # 1st field = # of timesteps to run MD :pre

		[Server replies]:

		cs->send(NATOMS,1) # msgID = 1 with 1 field
		cs->pack(1,1,Natoms) # 1st field = number of atoms :pre
		cs->pack_int(1,natoms) # 1st field = number of atoms :pre

		cs->send(EINIT,2) # msgID = 2 with 2 fields
		cs->pack(1,1,poteng) # 1st field = potential energy of system
		cs->pack(2,3*Natoms,x) # 2nd field = 3N coords of Natoms :pre
		cs->pack_double(1,poteng) # 1st field = potential energy of system
		cs->pack(2,3*natoms,x) # 2nd field = 3N coords of Natoms :pre

		cs->send(DISPLACE,1) # msgID = 3 with 1 field
		cs->pack(1,1,poteng) # 1st field = new potential energy of system :pre
		cs->pack_double(1,poteng) # 1st field = new potential energy of system :pre

		cs->send(ACCEPT,0) # msgID = 4 with no fields

doc/src/server_md.txt

+18 −17

Original line number	Diff line number	Diff line
		@@ -66,45 +66,46 @@ files for details on how LAMMPS uses these messages. See the
		examples/COUPLE/lammps_vasp/vasp_wrapper.py file for an example of how
		a quantum code (VASP) can use use these messages.

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

		enum{SETUP=1,STEP};
		enum{UNITS=1,DIM,NATOMS,NTYPES,BOXLO,BOXHI,BOXTILT,TYPES,COORDS,CHARGE};
		enum{FORCES=1,ENERGY,VIRIAL}; :pre
		enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
		enum{FORCES=1,ENERGY,VIRIAL,ERROR}; :pre

		[Client sends 2 kinds of messages]:

		# required fields: NATOMS, NTYPES, BOXLO, BOXHI, TYPES, COORDS
		# optional fields: others in 2nd enum above :pre
		# 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_string(UNITS,units) # units = "lj", "real", "metal", etc
		cs->pack_int(NATOMS,natoms) # total numer of atoms
		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(BOXLO,3,boxlo) # 3-vector of lower box bounds
		cs->pack(BOXHI,3,boxhi) # 3-vector of upper box bounds
		cs->pack(BOXTILT,3,boxtilt) # 3-vector of tilt factors for triclinic boxes
		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: BOXLO, BOXHI, BOXTILT :pre
		# optional fields: ORIGIN, BOX :pre

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

		cs->pack_int(NATOMS,natoms) # total numer of atoms
		cs->pack_int(NTYPES,ntypes) # number of atom types
		cs->pack(BOXLO,3,boxlo) # 3-vector of lower box bounds
		cs->pack(BOXTILT,3,boxtilt) # 3-vector of tilt factors for triclinic boxes :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

		[Server replies to either kind of message]:

		cs->send(msgID,3) # msgID = 1 with 3 fields
		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(VIRIAL,6,virial) # global virial tensor (6-vector) :pre
		cs->pack(VIRIAL,6,virial) # global virial tensor (6-vector)
		cs->pack(ERROR,6,virial) # server had an error (e.g. DFT non-convergence) :pre

		:line

src/MESSAGE/fix_client_md.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -31,7 +31,7 @@ using namespace FixConst;
		enum{OTHER,REAL,METAL}
		enum{SETUP=1,STEP};
		enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
		enum{FORCES=1,ENERGY,VIRIAL};
		enum{FORCES=1,ENERGY,VIRIAL,ERROR};

		/* ---------------------------------------------------------------------- */

src/MESSAGE/fix_client_md.h

+0 −1

Original line number	Diff line number	Diff line
		@@ -37,7 +37,6 @@ class FixClientMD : public Fix {
		double compute_scalar();

		private:
		void *cslib;
		int maxatom,units;
		double box[3][3];
		double eng;

src/MESSAGE/server_md.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -36,7 +36,7 @@ using namespace CSLIB_NS;
		enum{OTHER,REAL,METAL}
		enum{SETUP=1,STEP};
		enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
		enum{FORCES=1,ENERGY,VIRIAL};
		enum{FORCES=1,ENERGY,VIRIAL,ERROR};

		/* ---------------------------------------------------------------------- */

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