From 32509da7219643f1b46f491ea84e8a650155ef00 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 15 Apr 2016 16:06:25 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14828
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/Make.py                             |  2 +-
 src/USER-COLVARS/colvarproxy_lammps.cpp | 85 +++++++++++++++++++++++++
 src/USER-COLVARS/colvarproxy_lammps.h   | 23 ++++++-
 3 files changed, 108 insertions(+), 2 deletions(-)

diff --git a/src/Make.py b/src/Make.py
index 6ab41af99a..0a05255277 100755
--- a/src/Make.py
+++ b/src/Make.py
@@ -613,7 +613,7 @@ Syntax: Make.py switch args ...
     -atc, -awpmd, -colvars, -cuda, -gpu, -h5md,
     -meam, -poems, -python, -qmmm, -reax, -voronoi
   switches for build and makefile options:
-    -intel, -kokkos, -cc, -mpi, -fft, -jpg, -png
+    -intel, -kokkos, -cc, -flags, -mpi, -fft, -jpg, -png
 """
 
 # jmake switch
diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/USER-COLVARS/colvarproxy_lammps.cpp
index f42a2573d2..71786f060e 100644
--- a/src/USER-COLVARS/colvarproxy_lammps.cpp
+++ b/src/USER-COLVARS/colvarproxy_lammps.cpp
@@ -9,6 +9,8 @@
 #include "fix_colvars.h"
 
 #include "colvarmodule.h"
+#include "colvar.h"
+#include "colvarbias.h"
 #include "colvaratoms.h"
 #include "colvarproxy.h"
 #include "colvarproxy_lammps.h"
@@ -109,11 +111,20 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
   if (restart_output_prefix_str.rfind(".*") != std::string::npos)
     restart_output_prefix_str.erase(restart_output_prefix_str.rfind(".*"),2);
 
+#if defined(_OPENMP)
+  if (smp_thread_id() == 0) {
+    omp_init_lock(&smp_lock_state);
+  }
+#endif
+
   // initialize multi-replica support, if available
   if (replica_enabled()) {
     MPI_Comm_rank(inter_comm, &inter_me);
     MPI_Comm_size(inter_comm, &inter_num);
   }
+
+  if (cvm::debug())
+    log("Done initializing the colvars proxy object.\n");
 }
 
 
@@ -320,6 +331,80 @@ int colvarproxy_lammps::backup_file(char const *filename)
   }
 }
 
+
+#if defined(_OPENMP)
+
+
+// SMP support
+
+int colvarproxy_lammps::smp_enabled()
+{
+  return COLVARS_OK;
+}
+
+
+int colvarproxy_lammps::smp_colvars_loop()
+{
+  colvarmodule *cv = this->colvars;
+#pragma omp parallel for
+  for (size_t i = 0; i < cv->colvars_smp.size(); i++) {
+    if (cvm::debug()) {
+      cvm::log("Calculating colvar \""+cv->colvars_smp[i]->name+"\" on thread "+cvm::to_str(smp_thread_id())+"\n");
+    }
+    cv->colvars_smp[i]->calc_cvcs(cv->colvars_smp_items[i], 1);
+  }
+  return cvm::get_error();
+}
+
+
+int colvarproxy_lammps::smp_biases_loop()
+{
+  colvarmodule *cv = this->colvars;
+#pragma omp parallel for
+  for (size_t i = 0; i < cv->biases.size(); i++) {
+    if (cvm::debug()) {
+      cvm::log("Calculating bias \""+cv->biases[i]->name+"\" on thread "+cvm::to_str(smp_thread_id())+"\n");
+    }
+    cv->biases[i]->update();
+  }
+  return cvm::get_error();
+}
+
+
+int colvarproxy_lammps::smp_thread_id()
+{
+  return omp_get_thread_num();
+}
+
+
+int colvarproxy_lammps::smp_num_threads()
+{
+  return omp_get_max_threads();
+}
+
+
+int colvarproxy_lammps::smp_lock()
+{
+  omp_set_lock(&smp_lock_state);
+  return COLVARS_OK;
+}
+
+
+int colvarproxy_lammps::smp_trylock()
+{
+  return omp_test_lock(&smp_lock_state) ? COLVARS_OK : COLVARS_ERROR;
+}
+
+
+int colvarproxy_lammps::smp_unlock()
+{
+  omp_unset_lock(&smp_lock_state);
+  return COLVARS_OK;
+}
+
+#endif
+
+
 // multi-replica support
 
 void colvarproxy_lammps::replica_comm_barrier() {
diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/USER-COLVARS/colvarproxy_lammps.h
index 25ffa2502a..6368e965f7 100644
--- a/src/USER-COLVARS/colvarproxy_lammps.h
+++ b/src/USER-COLVARS/colvarproxy_lammps.h
@@ -5,6 +5,7 @@
 
 #include "colvarmodule.h"
 #include "colvarproxy.h"
+#include "colvarvalue.h"
 
 #include "lammps.h"
 #include "domain.h"
@@ -16,8 +17,12 @@
 #include <vector>
 #include <iostream>
 
+#if defined(_OPENMP)
+#include <omp.h>
+#endif
+
 #ifndef COLVARPROXY_VERSION
-#define COLVARPROXY_VERSION "2016-02-28"
+#define COLVARPROXY_VERSION "2016-04-08"
 #endif
 
 /* struct for packed data communication of coordinates and forces. */
@@ -130,6 +135,22 @@ class colvarproxy_lammps : public colvarproxy {
 
   // implementation of optional methods from base class
  public:
+
+#if defined(_OPENMP)
+  // SMP support
+  int smp_enabled();
+  int smp_colvars_loop();
+  int smp_biases_loop();
+  int smp_thread_id();
+  int smp_num_threads();
+protected:
+  omp_lock_t smp_lock_state;
+public:
+  int smp_lock();
+  int smp_trylock();
+  int smp_unlock();
+#endif
+
   // Multi-replica support
   // Indicate if multi-replica support is available and active
   virtual bool replica_enabled() { return (inter_comm != MPI_COMM_NULL); }