more debugging for plugin mode

examples/mdi/README

@@ -2,32 +2,47 @@ These are examples that work the MDI package in LAMMPS which uses the
 MolSSI MDI library for coupling codes together and communicating
 between them with MDI messages.
 
-To use the serial_drive.py example you will need Python 3 with Numpy
-and mpi4py available in your Python.  Make sure LAMMPS and Python are
-using same the same version of MPI.
-
 In MDI lingo, one code is the driver and another code is the engine.
 The 2 codes can be written in any language; C++ (LAMMPS) and Python
-are illustrated here.  The 2 codes can be run on different numbers of
-processors.  
-
-The 2 codes can communicate either via TCP (sockets) or via MPI.  For
-the TCP case, the driver and engine need to be launched separately,
+are illustrated here.  The 2 codes can each be stand-alone codes, in
+which case they can be run on different numbers of processors.  The 2
+codes can communicate either via TCP (sockets) or via MPI.  For the
+TCP case, the driver and engine need to be launched separately,
 e.g. in 2 windows on your desktop machine.  For the MPI case, a single
 mpirun command launches both codes.
 
-The example run commands below have variants for these options.
+Alternatively the engine code can be a plugin library which the driver
+code loads, in which case the driver and engine run on the same
+processors.
+
+LAMMPS supports operating in all these modes.  It can be an engine
+operating either as a stand-alone code or as a plugin.  It can also be
+a driver and couple to an engine that is either a stand-alone code or
+a plugin.  Examples for all these use cases are in this directory.
+The example run commands below illustrate all the variants.
+
+To use LAMMPS as a plugin engine, you must build it as a shared library.
+Something like this:
+
+cd src
+make yes-mdi
+make mode=shlib mpi
+
+To use the serial_driver.py example you will need Python 3 with Numpy
+and mpi4py available in your Python.  Make sure LAMMPS and Python are
+using same the same version of MPI.
 
 -------------------------------------------------
 -------------------------------------------------
 
-* Example #1 = run AIMD with 2 instances of LAMMPS as driver and engine
-               as an engine, LAMMPS is a surrogate for a quantum code
+* Example #1 = run ab inito MD (AIMD)
+  2 instances of LAMMPS operate as a driver and engine
+  as an engine, LAMMPS is a surrogate for a quantum code
 
 Note that the 2 input scripts in.aimd.alone and in.aimd.driver
 have an option for running in NVE vs NPT mode.  Comment in/out
 the appropriate line to change modes.  Nothing needs to be
-changed in the 3rd input script in.aimd.engine.
+changed in the in.aimd.engine or in.aimd.engine.plugin scripts.
 
 ---
 
@@ -83,13 +98,13 @@ Run in plugin mode: 3 procs
 -------------------------------------------------
 
 * Example #2 = Python driver runs sequence of unrelated LAMMPS calculations
-               calcs can be single-point, MD runs, or minimizations
+  Each calculation can be a single-point evaluation, an MD run, or a minimization.
 
 The sequence_driver.py code allows for optional switches in addition
 to -mdi (required) and the -plugin and -plugin_args switches which are
 used to link to an engine as a plugin library.  The example run
 commands below just use the default values of the optional switches.
-The switches are also explained the top of the file; the info is
+The switches are also explained at the top of the file; the info is
 copied here:
 
 #   -n 10
@@ -163,7 +178,7 @@ The aimd_driver.py code allows for an optional switch in addition to
 -mdi (required) and the -plugin and -plugin_args swiches which are
 used to link to the 2 engines as a plugin libraries.  The example run
 commands below use the default values of the optional switch.  The
-switches are also explained the top of the file; the info is copied
+switch is also explained the top of the file; the info is copied
 here:
 
 #   -nsteps 5

examples/mdi/in.aimd.driver.plugin

@@ -23,12 +23,12 @@ fix		1 all nve
 # NPT
 #fix             1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
 
-fix             2 all mdi/aimd
+fix             2 all mdi/aimd plugin
 fix_modify      2 energy yes virial yes
 
 thermo_style    custom step temp pe etotal press vol
 thermo          1
 
-mdi/plugin      lammps &
-                args '-mdi "-role ENGINE -name lammps -method LINK"' &
+mdi/plugin      lammps mdi "-role ENGINE -name lammps -method LINK" &
+                infile in.aimd.engine extra "-log log.aimd.engine.plugin" &
                 command "run 5"

src/MDI/fix_mdi_aimd.cpp

@@ -30,7 +30,7 @@ enum{NATIVE,REAL,METAL};   // LAMMPS units which MDI supports
 FixMDIAimd::FixMDIAimd(LAMMPS *lmp, int narg, char **arg) :
     Fix(lmp, narg, arg)
 {
-  if (narg != 3) error->all(FLERR, "Illegal fix mdi/aimd command");
+  if (narg > 4) error->all(FLERR, "Illegal fix mdi/aimd command");
 
   scalar_flag = 1;
   global_freq = 1;
@@ -39,6 +39,14 @@ FixMDIAimd::FixMDIAimd(LAMMPS *lmp, int narg, char **arg) :
   virial_global_flag = 1;
   thermo_energy = thermo_virial = 1;
 
+  // check for plugin arg
+
+  plugin = 0;
+  if (narg == 4) {
+    if (strcmp(arg[3],"plugin") == 0) plugin = 1;
+    else error->all(FLERR, "Illegal fix mdi/aimd command");
+  }
+
   // check requirements for LAMMPS to work with MDI as an engine
 
   if (atom->tag_enable == 0)
@@ -67,10 +75,12 @@ FixMDIAimd::FixMDIAimd(LAMMPS *lmp, int narg, char **arg) :
 
   unit_conversions();
 
-  // connect to MDI engine
+  // connect to MDI engine, only if engine is stand-alone code
 
-  // MDI_Accept_communicator(&mdicomm);
-  // if (mdicomm <= 0) error->all(FLERR, "Unable to connect to MDI engine");
+  if (!plugin) {
+    MDI_Accept_communicator(&mdicomm);
+    if (mdicomm <= 0) error->all(FLERR, "Unable to connect to MDI engine");
+  }
 
   nprocs = comm->nprocs;
 }
@@ -79,10 +89,12 @@ FixMDIAimd::FixMDIAimd(LAMMPS *lmp, int narg, char **arg) :
 
 FixMDIAimd::~FixMDIAimd()
 {
-  // send exit command to engine
+  // send exit command to engine, only if engine is stand-alone code
 
-  //int ierr = MDI_Send_command("EXIT",mdicomm);
-  //if (ierr) error->all(FLERR,"MDI: EXIT command");
+  if (!plugin) {
+    int ierr = MDI_Send_command("EXIT",mdicomm);
+    if (ierr) error->all(FLERR,"MDI: EXIT command");
+  }
 
   // clean up
 

src/MDI/fix_mdi_aimd.h

@@ -44,6 +44,8 @@ class FixMDIAimd : public Fix {
 
  private:
   int nprocs;
+  int plugin;
+
   int eflag_caller;
   double engine_energy;
   int lmpunits;
@@ -65,7 +67,6 @@ class FixMDIAimd : public Fix {
 
   void reallocate();
   void unit_conversions();
-
 };
 
 }

src/MDI/mdi_plugin.cpp

@@ -37,27 +37,52 @@ void MDIPlugin::command(int narg, char **arg)
   if (narg < 1) error->all(FLERR,"Illegal mdi/plugin command");
 
   char *plugin_name = arg[0];
-  char *plugin_args = nullptr;
-  plugin_command = nullptr;
 
-  printf("NARG %d\n",narg);
+  char *mdi_arg = nullptr;
+  char *infile_arg = nullptr;
+  char *extra_arg = nullptr;
+  lammps_command = nullptr;
 
   int iarg = 1;
   while (iarg < narg) {
-    if (strcmp(arg[iarg],"args") == 0) {
+    if (strcmp(arg[iarg],"mdi") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal mdi/plugin command");
-      plugin_args = arg[iarg+1];
+      mdi_arg = arg[iarg+1];
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"infile") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal mdi/plugin command");
+      infile_arg = arg[iarg+1];
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"extra") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal mdi/plugin command");
+      extra_arg = arg[iarg+1];
       iarg += 2;
     } else if (strcmp(arg[iarg],"command") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal mdi/plugin command");
-      plugin_command = arg[iarg+1];
+      int n = strlen(arg[iarg+1]) + 1;
+      lammps_command = new char[n];
+      strcpy(lammps_command,arg[iarg+1]);
       iarg += 2;
     } else error->all(FLERR,"Illegal mdi/plugin command");
   }
 
-  // error if no command was specified
+  // error checks
 
-  if (!plugin_command) error->all(FLERR,"MDI/plugin must specify command");
+  if (!mdi_arg || !infile_arg || !lammps_command) 
+    error->all(FLERR,"MDI/plugin must specify mdi, infile, command keywords");
+
+  // build full plugin_args string for args to plugin library
+
+  int n = strlen(mdi_arg) + strlen(infile_arg) + strlen(extra_arg) + 16;
+  char *plugin_args = new char[n];
+  strcat(plugin_args,"-mdi \"");
+  strcat(plugin_args,mdi_arg);
+  strcat(plugin_args,"\" -in ");
+  strcat(plugin_args,infile_arg);
+  if (extra_arg) {
+    strcat(plugin_args," ");
+    strcat(plugin_args,extra_arg);
+  }
 
   // find FixMDIAimd instance so can reset its mdicomm
 
@@ -72,6 +97,8 @@ void MDIPlugin::command(int narg, char **arg)
   printf("ARGS %s\n",plugin_args);
 
   MDI_Launch_plugin(plugin_name,plugin_args,world,plugin_wrapper,(void *)this);
+
+  delete [] plugin_args;
 }
 
 /* ----------------------------------------------------------------------
@@ -81,25 +108,27 @@ void MDIPlugin::command(int narg, char **arg)
 ---------------------------------------------------------------------- */
 
 int MDIPlugin::plugin_wrapper(void *pmpicomm, MDI_Comm mdicomm, 
-                              void *ptr)
+                              void *vptr)
 {
   printf("INSIDE CALLBACK\n");
 
   MPI_Comm mpicomm = *(MPI_Comm *) pmpicomm;
-  MDIPlugin *thisptr = (MDIPlugin *) ptr;
-  LAMMPS *lammps = thisptr->lmp;
+  MDIPlugin *ptr = (MDIPlugin *) vptr;
+  LAMMPS *lammps = ptr->lmp;
+  char *lammps_command = ptr->lammps_command;
  
   // set FixMDIAimd mdicomm to this mdicomm
 
-  FixMDIAimd *aimdptr = (FixMDIAimd *) (thisptr->fixptr);
+  FixMDIAimd *aimdptr = (FixMDIAimd *) (ptr->fixptr);
   aimdptr->mdicomm = mdicomm;
 
   // invoke the specified LAMMPS command
   // that operation will issue MDI commands to the plugin engine
 
-  printf("PRE RUN command\n");
+  printf("PRE RUN command: %s\n",lammps_command);
 
-  lammps->input->one(thisptr->plugin_command);
+  lammps->input->one(lammps_command);
+  delete [] lammps_command;
 
   // send MDI exit to plugin, which unloads the plugin
 

src/MDI/mdi_plugin.h

@@ -31,7 +31,7 @@ class MDIPlugin : public Command {
   void command(int, char **) override;
 
  private:
-  char *plugin_command;
+  char *lammps_command;
   class Fix *fixptr;
 
   static int plugin_wrapper(void *, MDI_Comm, void *);

src/library.cpp

@@ -172,6 +172,9 @@ void *lammps_open(int argc, char **argv, MPI_Comm comm, void **ptr)
   lammps_mpi_init();
   if (ptr) ptr_argument_warning();
 
+  printf("LAMMPS instantiate argc %d argv[1] %s argv[2] %s\n",
+         argc,argv[1],argv[2]);
+
 #ifdef LAMMPS_EXCEPTIONS
   try
   {
@@ -183,7 +186,9 @@ void *lammps_open(int argc, char **argv, MPI_Comm comm, void **ptr)
     if (ptr) *ptr = nullptr;
   }
 #else
+  printf("PRE-INSTANTIATE\n");
   lmp = new LAMMPS(argc, argv, comm);
+  printf("POST-INSTANTIATE %p\n",lmp);
   if (ptr) *ptr = (void *) lmp;
 #endif
   return (void *) lmp;