docs for MD protocol enhancements

doc/src/server_mc.txt

@@ -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->send(EINIT,2)         # msgID = 2 with 2 fields
+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->send(DISPLACE,1)      # msgID = 3 with 1 field
+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

@@ -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

@@ -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

@@ -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

@@ -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};
 
 /* ---------------------------------------------------------------------- */