added support for LAMMPS as MDI AIMD driver

src/MDI/fix_mdi_aimd.cpp

@@ -0,0 +1,143 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/ Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "error.h"
+#include "fix_mdi_aimd.h"
+#include "atom.h"
+#include "comm.h"
+#include "domain.h"
+#include "force.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+/* ---------------------------------------------------------------------- */
+
+FixMDIAimd::FixMDIAimd(LAMMPS *lmp, int narg, char **arg) :
+    Fix(lmp, narg, arg)
+{
+  if (narg != 3) error->all(FLERR, "Illegal fix mdi/aimd command");
+
+  scalar_flag = 1;
+  global_freq = 1;
+  extscalar = 1;
+  energy_global_flag = 1;
+  virial_global_flag = 1;
+  thermo_energy = thermo_virial = 1;
+
+  // connect to MDI engine
+
+  MDI_Accept_communicator(&engine);
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixMDIAimd::~FixMDIAimd()
+{
+  // send exit command to engine
+
+  MDI_Send_command("EXIT",engine);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixMDIAimd::setmask()
+{
+  int mask = 0;
+  mask |= PRE_REVERSE;
+  mask |= POST_FORCE;
+  mask |= MIN_POST_FORCE;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixMDIAimd::setup(int vflag)
+{
+  post_force(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixMDIAimd::setup_pre_reverse(int eflag, int vflag)
+{
+  pre_reverse(eflag,vflag);
+}
+
+/* ----------------------------------------------------------------------
+   store eflag, so can use it in post_force to request energy
+------------------------------------------------------------------------- */
+
+void FixMDIAimd::pre_reverse(int eflag, int /*vflag*/)
+{
+  eflag_caller = eflag;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixMDIAimd::post_force(int vflag)
+{
+  int eflag = eflag_caller;
+  ev_init(eflag,vflag);
+
+  // send current coords to MDI engine
+  // NOTE: need to gather them to proc 0
+
+  MDI_Send_command(">COORDS",engine);
+  MDI_Send(&atom->x[0][0],3*atom->nlocal,MDI_DOUBLE,engine);
+
+  // trigger engine to evaluate forces,energy,pressure for current system
+
+  MDI_Send_command("EVAL",engine);
+
+  // request energy from MDI engine
+
+  if (eflag_global) {
+    MDI_Send_command("<PE",engine);
+    MDI_Recv(&engine_energy,1,MDI_DOUBLE,engine);
+  }
+
+  // request pressure tensor from MDI engine, convert to virial
+
+  if (vflag_global) {
+    double ptensor[6];
+    MDI_Send_command("<PTENSOR",engine);
+    MDI_Recv(ptensor,6,MDI_DOUBLE,engine);
+
+    double volume = domain->xprd * domain->yprd * domain->zprd;
+    for (int i = 0; i < 6; i++)
+      virial[i] = ptensor[i] * volume / force->nktv2p;
+  }
+
+  // request forces from MDI engine
+  // NOTE: need to scatter to procs, then add to my local forces
+
+  MDI_Send_command("<FORCES",engine);
+  MDI_Recv(&atom->f[0][0],3*atom->nlocal,MDI_DOUBLE,engine);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixMDIAimd::min_post_force(int vflag)
+{
+  post_force(vflag);
+}
+
+/* ----------------------------------------------------------------------
+   energy from MDI engine
+------------------------------------------------------------------------- */
+
+double FixMDIAimd::compute_scalar()
+{
+  return engine_energy;
+}

src/MDI/fix_mdi_aimd.h

@@ -0,0 +1,55 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/ Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+// clang-format off
+FixStyle(mdi/aimd,FixMDIAimd);
+// clang-format on
+#else
+
+#ifndef LMP_FIX_MDI_AIMD_H
+#define LMP_FIX_MDI_AIMD_H
+
+#include "fix.h"
+#include <mdi.h>
+
+namespace LAMMPS_NS {
+
+class FixMDIAimd : public Fix {
+ public:
+  FixMDIAimd(class LAMMPS *, int, char **);
+  ~FixMDIAimd();
+  int setmask();
+
+  void setup(int);
+  void setup_pre_reverse(int, int);
+  void pre_reverse(int, int);
+  void post_force(int);
+  void min_post_force(int);
+  double compute_scalar();
+
+ private:
+  int eflag_caller;
+  double engine_energy;
+
+  MDI_Comm engine;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/

src/MDI/fix_mdi_engine.cpp

@@ -378,6 +378,9 @@ char *FixMDIEngine::engine_mode(const char *node)
     fprintf(logfile,"MDI ENGINE MODE: %i\n",node);
   */
 
+  printf("ENG NODE ENTRY eng/driver %s %s %d %d\n",
+         node,target_node,strlen(node),strlen(target_node));
+
   // do not process commands if engine and driver are not at same node
   // target_node = node that driver has set via a @ command
   // current_node = node that engine (LAMMPS) has set
@@ -402,10 +405,14 @@ char *FixMDIEngine::engine_mode(const char *node)
 
     // execute the command
 
+    printf("RECV CMD %s\n",command);
     this->execute_command(command, driver_socket);
 
     // check if the target node is something other than the current node
 
+    printf("ENG NODES eng/driver %s %s %d %d\n",
+           node,target_node,strlen(node),strlen(target_node));
+
     if (strcmp(target_node, "\0") != 0 && strcmp(target_node, current_node) != 0)
       local_exit_flag = true;
   }

src/MDI/fix_mdi_engine2.cpp

@@ -0,0 +1,79 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/ Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Taylor Barnes (MolSSI)
+   MolSSI Driver Interface (MDI) support for LAMMPS
+------------------------------------------------------------------------- */
+
+#include "error.h"
+#include "fix_mdi_engine2.h"
+#include "mdi_engine2.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+/* ---------------------------------------------------------------------- */
+
+FixMDIEngine2::FixMDIEngine2(LAMMPS *lmp, int narg, char **arg) :
+    Fix(lmp, narg, arg)
+{
+  if (narg != 3) error->all(FLERR, "Illegal fix mdi/engine command");
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixMDIEngine2::setmask()
+{
+  int mask = 0;
+  mask |= POST_INTEGRATE;
+  mask |= POST_FORCE;
+  mask |= MIN_PRE_FORCE;
+  mask |= MIN_POST_FORCE;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixMDIEngine2::min_setup(int vflag)
+{
+  mdi_engine->engine_node("@FORCES");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixMDIEngine2::post_integrate()
+{
+  mdi_engine->engine_node("@COORDS");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixMDIEngine2::min_pre_force(int vflag)
+{
+  mdi_engine->engine_node("@COORDS");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixMDIEngine2::min_post_force(int vflag)
+{
+  mdi_engine->engine_node("@FORCES");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixMDIEngine2::post_force(int vflag)
+{
+  mdi_engine->engine_node("@FORCES");
+}

src/MDI/fix_mdi_engine2.h

@@ -0,0 +1,81 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/ Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+// clang-format off
+FixStyle(mdi/engine2, FixMDIEngine2);
+// clang-format on
+#else
+
+#ifndef LMP_FIX_MDI_ENGINE2_H
+#define LMP_FIX_MDI_ENGINE2_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixMDIEngine2 : public Fix {
+ public:
+  class MDIEngine2 *mdi_engine;
+
+  FixMDIEngine2(class LAMMPS *, int, char **);
+  ~FixMDIEngine2() {}
+  int setmask();
+  void init() {}
+
+  void min_setup(int);
+  void post_integrate();
+  void post_force(int);
+  void min_pre_force(int);
+  void min_post_force(int);
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.
+
+E: Potential energy ID for fix mdi does not exist
+
+Self-explanatory.
+
+E: Cannot use MDI command without atom IDs
+
+Self-explanatory.
+
+E: MDI command requires consecutive atom IDs
+
+Self-explanatory.
+
+E: Unable to connect to driver
+
+Self-explanatory.
+
+E: Unable to ... driver
+
+Self-explanatory.
+
+E: Unknown command from driver
+
+The driver sent a command that is not supported by the LAMMPS
+interface.  In some cases this might be because a nonsensical
+command was sent (i.e. "SCF").  In other cases, the LAMMPS
+interface might benefit from being expanded.
+
+*/

src/MDI/library_mdi.cpp

@@ -13,11 +13,13 @@
 
 // ----------------------------------------------------------------------
 // MolSSI Driver Interface functions
+// these are added to LAMMPS library interface when MDI package is included
 // ----------------------------------------------------------------------
 
 #include "library_mdi.h"
 
 // needed to enable MPI support
+
 #define LAMMPS_LIB_MPI 1
 #include "library.h"
 
@@ -27,6 +29,8 @@
 
 using namespace LAMMPS_NS;
 
+/* ---------------------------------------------------------------------- */
+
 /** Initialize an instance of LAMMPS as an MDI plugin
  *
 \verbatim embed:rst
@@ -51,6 +55,7 @@ command-line argument, which must be provided by the MDI driver.
 int MDI_Plugin_init_lammps()
 {
   // initialize MDI
+
   int mdi_argc;
   char **mdi_argv;
   if (MDI_Plugin_get_argc(&mdi_argc)) MPI_Abort(MPI_COMM_WORLD, 1);
@@ -58,30 +63,36 @@ int MDI_Plugin_init_lammps()
   if (MDI_Init(&mdi_argc, &mdi_argv)) MPI_Abort(MPI_COMM_WORLD, 1);
 
   // get the MPI intra-communicator for this code
+
   MPI_Comm mpi_world_comm = MPI_COMM_WORLD;
   if (MDI_MPI_get_world_comm(&mpi_world_comm)) MPI_Abort(MPI_COMM_WORLD, 1);
 
   // find the -in argument
+
   int iarg = 0;
   char *filename;
   bool found_filename = false;
   while (iarg < mdi_argc && !found_filename) {
 
-    if ((strcmp(mdi_argv[iarg], "-in") == 0) || (strcmp(mdi_argv[iarg], "-i") == 0)) {
+    if ((strcmp(mdi_argv[iarg], "-in") == 0) || 
+        (strcmp(mdi_argv[iarg], "-i") == 0)) {
 
       if (iarg + 2 > mdi_argc) MPI_Abort(MPI_COMM_WORLD, 1);
       filename = mdi_argv[iarg + 1];
       found_filename = true;
 
       // remove -in argument from the command list
+
       mdi_argc -= 2;
-      for (int jarg = iarg; jarg < mdi_argc; jarg++) mdi_argv[jarg] = mdi_argv[jarg + 2];
+      for (int jarg = iarg; jarg < mdi_argc; jarg++) 
+        mdi_argv[jarg] = mdi_argv[jarg + 2];
     }
     iarg++;
   }
   if (!found_filename) MPI_Abort(MPI_COMM_WORLD, 1);
 
   // create and run a LAMMPS instance
+
   void *lmp = nullptr;
   if (lammps_config_has_mpi_support() > 0)
     lmp = lammps_open(mdi_argc, mdi_argv, mpi_world_comm, nullptr);
@@ -93,6 +104,8 @@ int MDI_Plugin_init_lammps()
   return 0;
 }
 
+/* ---------------------------------------------------------------------- */
+
 /** Execute an MDI command
  *
 \verbatim embed:rst

src/MDI/mdi_engine2.h

@@ -0,0 +1,128 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/ Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMMAND_CLASS
+// clang-format off
+CommandStyle(mdi,MDIEngine2);
+// clang-format on
+#else
+
+#ifndef LMP_MDI_ENGINE2_H
+#define LMP_MDI_ENGINE2_H
+
+#include "command.h"
+#include "mdi.h"
+
+namespace LAMMPS_NS {
+
+class MDIEngine2 : public Command {
+ public:
+  MDIEngine2(LAMMPS *lmp) : Command(lmp) {}
+  virtual ~MDIEngine2() {}
+  void command(int, char **);
+
+  int execute_command(const char *command, MDI_Comm mdicomm);
+  void engine_node(const char *node);
+
+ private:
+  int lmpunits;    // REAL or METAL or NATIVE
+  int root;        // 1 for proc 0, otherwise 0
+
+  // state of MDI engine
+
+  int mode;              // which mode engine is in (DEFAULT,MD,OPTG,etc)
+  char *mdicmd;          // current MDI command being processed
+  char *node_engine;     // which node engine is at
+  char *node_driver;     // which node driver has requested
+  bool node_match;       // true if driver and engine node currently match
+  bool exit_command;     // true if EXIT command received from driver
+
+  MDI_Comm mdicomm;
+  class FixMDIEngine2 *mdi_fix;
+
+  char *id_ke,*id_pe,*id_press;
+  class Irregular *irregular;
+  class Minimize *minimizer;
+  class Compute *ke,*pe,*press;
+
+  int length_param;         // LENGTH command value used by other commands
+
+  // unit conversion factors;
+
+  double lmp2mdi_length,mdi2lmp_length;
+  double lmp2mdi_energy,mdi2lmp_energy;
+  double lmp2mdi_velocity,mdi2lmp_velocity;
+  double lmp2mdi_force,mdi2lmp_force;
+  double lmp2mdi_pressure,mdi2lmp_pressure;
+  double lmp2mdi_virial,mdi2lmp_virial;
+
+  // buffers for MDI comm
+
+  int maxbuf;
+  double *buf1,*buf1all;
+  double *buf3,*buf3all;
+  int *ibuf1,*ibuf1all;
+
+  // class methods
+
+  void mdi_engine(int, char **);
+
+  void mdi_commands();
+  void mdi_md();
+  void mdi_optg();
+
+  void receive_double1(int);
+  void receive_int1(int);
+  void receive_double3(int, int);
+  void send_double1(int);
+  void send_int1(int);
+  void send_double3(int);
+
+  void send_labels();
+
+  void send_energy();
+  void send_pe();
+  void send_ke();
+  void send_cell();
+  void receive_cell();
+  void send_celldispl();
+  void receive_celldispl();
+
+  void length_command();
+  void single_command();
+  void many_commands();
+  void infile();
+  void evaluate();
+  void reset_box();
+  void create_atoms();
+  void send_pressure();
+  void send_ptensor();
+
+  void unit_conversions();
+  void reallocate();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+*/

src/comm.cpp

@@ -739,7 +739,8 @@ double Comm::get_comm_cutoff()
       error->warning(FLERR,"Communication cutoff adjusted to {}",maxcommcutoff);
   }
 
-  // Check maximum interval size for neighbor multi
+  // check maximum interval size for neighbor multi
+
   if (neighbor->interval_collection_flag) {
     for (int i = 0; i < neighbor->ncollections; i++){
       maxcommcutoff = MAX(maxcommcutoff, neighbor->collection2cut[i]);