Merge pull request #1928 from akohlmey/collected-small-fixes

Collected small fixes and updates for the next patch release

doc/src/kspace_style.rst

@@ -406,8 +406,8 @@ interactions. Vacuum boundary conditions are not currently supported.
 
 The *ewald/disp*\ , *ewald*\ , *pppm*\ , and *msm* styles support
 non-orthogonal (triclinic symmetry) simulation boxes. However,
-triclinic simulation cells may not yet be supported by suffix versions
-of these styles.
+triclinic simulation cells may not yet be supported by all suffix
+versions of these styles.
 
 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.

doc/src/server_md.txt

@@ -1,150 +0,0 @@
-"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

@@ -69,7 +69,7 @@ CommandStyle(kim_init,KimInit)
 #include <string>
 
 // Forward declaration.
-class KIM_Model;
+typedef struct KIM_Model KIM_Model;
 
 namespace LAMMPS_NS {
 

src/MESSAGE/fix_client_md.cpp

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

src/MESSAGE/server_mc.cpp

@@ -13,6 +13,7 @@
 
 #include "server_mc.h"
 #include "atom.h"
+#include "domain.h"
 #include "update.h"
 #include "integrate.h"
 #include "input.h"
@@ -43,17 +44,17 @@ void ServerMC::loop()
 
   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
 
   input->one("run 0");
 
-  //update->whichflag = 1;
-  //lmp->init();
-
   // loop on messages
   // receive a message, process it, send return message if necessary
 
@@ -123,8 +124,6 @@ void ServerMC::loop()
 
       int nsteps = cs->unpack_int(1);
 
-      //input->one("run 100");
-
       update->nsteps = nsteps;
       update->firststep = update->ntimestep;
       update->laststep = update->ntimestep + nsteps;

src/MESSAGE/server_md.cpp

@@ -48,7 +48,7 @@ ServerMD::ServerMD(LAMMPS *lmp) : Pointers(lmp)
 
   if (!atom->map_style) error->all(FLERR,"Server md requires atom map");
   if (atom->tag_enable == 0) error->all(FLERR,"Server md requires atom IDs");
-  if (sizeof(tagint) != 4) error->all(FLERR,"Server md requires 4-byte atom IDs");
+  if (sizeof(tagint) != 4) error->all(FLERR,"Server md requires 32-bit atom IDs");
 
   if (strcmp(update->unit_style,"real") == 0) units = REAL;
   else if (strcmp(update->unit_style,"metal") == 0) units = METAL;

src/USER-INTEL/pppm_disp_intel.cpp

@@ -62,6 +62,7 @@ enum{FORWARD_IK, FORWARD_AD, FORWARD_IK_PERATOM, FORWARD_AD_PERATOM,
 PPPMDispIntel::PPPMDispIntel(LAMMPS *lmp) : PPPMDisp(lmp)
 {
   suffix_flag |= Suffix::INTEL;
+  triclinic_support = 0;
 
   order = 7;
   order_6 = 7; //sets default stencil sizes to 7

src/USER-INTEL/pppm_intel.cpp

@@ -208,16 +208,23 @@ void PPPMIntel::compute_first(int eflag, int vflag)
 
   // find grid points for all my particles
   // map my particle charge onto my local 3d density grid
+  // optimized versions can only be used for orthogonal boxes
 
-  if (fix->precision() == FixIntel::PREC_MODE_MIXED) {
-    particle_map<float,double>(fix->get_mixed_buffers());
-    make_rho<float,double>(fix->get_mixed_buffers());
-  } else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) {
-    particle_map<double,double>(fix->get_double_buffers());
-    make_rho<double,double>(fix->get_double_buffers());
+  if (triclinic) {
+    PPPM::particle_map();
+    PPPM::make_rho();
   } else {
-    particle_map<float,float>(fix->get_single_buffers());
-    make_rho<float,float>(fix->get_single_buffers());
+
+    if (fix->precision() == FixIntel::PREC_MODE_MIXED) {
+      particle_map<float,double>(fix->get_mixed_buffers());
+      make_rho<float,double>(fix->get_mixed_buffers());
+    } else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) {
+      particle_map<double,double>(fix->get_double_buffers());
+      make_rho<double,double>(fix->get_double_buffers());
+    } else {
+      particle_map<float,float>(fix->get_single_buffers());
+      make_rho<float,float>(fix->get_single_buffers());
+    }
   }
 
   // all procs communicate density values from their ghost cells
@@ -258,21 +265,26 @@ void PPPMIntel::compute_second(int /*eflag*/, int /*vflag*/)
   int i,j;
 
   // calculate the force on my particles
+  // optimized versions can only be used for orthogonal boxes
 
-  if (differentiation_flag == 1) {
-    if (fix->precision() == FixIntel::PREC_MODE_MIXED)
-      fieldforce_ad<float,double>(fix->get_mixed_buffers());
-    else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE)
-      fieldforce_ad<double,double>(fix->get_double_buffers());
-    else
-      fieldforce_ad<float,float>(fix->get_single_buffers());
+  if (triclinic) {
+    PPPM::fieldforce();
   } else {
-    if (fix->precision() == FixIntel::PREC_MODE_MIXED)
-      fieldforce_ik<float,double>(fix->get_mixed_buffers());
-    else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE)
-      fieldforce_ik<double,double>(fix->get_double_buffers());
-    else
-      fieldforce_ik<float,float>(fix->get_single_buffers());
+    if (differentiation_flag == 1) {
+      if (fix->precision() == FixIntel::PREC_MODE_MIXED)
+        fieldforce_ad<float,double>(fix->get_mixed_buffers());
+      else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE)
+        fieldforce_ad<double,double>(fix->get_double_buffers());
+      else
+        fieldforce_ad<float,float>(fix->get_single_buffers());
+    } else {
+      if (fix->precision() == FixIntel::PREC_MODE_MIXED)
+        fieldforce_ik<float,double>(fix->get_mixed_buffers());
+      else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE)
+        fieldforce_ik<double,double>(fix->get_double_buffers());
+      else
+        fieldforce_ik<float,float>(fix->get_single_buffers());
+    }
   }
 
   // extra per-atom energy/virial communication

src/min_fire.cpp

@@ -314,7 +314,7 @@ int MinFire::iterate(int maxiter)
       for (int i = 0; i < nlocal; i++)
         v[i][0] = v[i][1] = v[i][2] = 0.0;
     }
-    
+
     // min dtv over replicas, if necessary
     // this communicator would be invalid for multiprocess replicas
 

src/pair_hybrid.cpp

@@ -742,7 +742,7 @@ void PairHybrid::read_restart(FILE *fp)
     keywords[m] = new char[n];
     if (me == 0) utils::sfread(FLERR,keywords[m],sizeof(char),n,fp,NULL,error);
     MPI_Bcast(keywords[m],n,MPI_CHAR,0,world);
-    styles[m] = force->new_pair(keywords[m],0,dummy);
+    styles[m] = force->new_pair(keywords[m],1,dummy);
     styles[m]->read_restart_settings(fp);
     // read back per style special settings, if present
     special_lj[m] = special_coul[m] = NULL;