Update Colvars to version 2017-10-11

Notable features are the umbrella-integration based free energy estimator for
eABF, and the traditional thermodynamic integration estimator now available
for umbrella sampling, SMD, metadynamics.  Also included are several small fixes.

Below is a list of relevant commits in the Colvars repository since the last update.

321d06a 2017-10-10 Add macros to manage colvarscript commands [Giacomo Fiorin]
26c3bec 2017-10-09 Document coming availability of Lepton in LAMMPS [Giacomo Fiorin]
cc8f249 2017-10-04 Clarify that SMP depends on code build [Giacomo Fiorin]
0b2ffac 2017-10-04 Summarize colvar definition options, clarify some details [Giacomo Fiorin]
28002e0 2017-10-01 Separate writing of restart file from other output (e.g. PMFs) [Giacomo Fiorin]
92f7c1d 2017-10-01 Deprecate colvarsTrajAppend [Giacomo Fiorin]
12a707f 2017-09-26 Accurate Jacobian calculation for RMSD variants [Jérôme Hénin]
fe389c9 2017-09-21 Allow subtractAppliedForce with extended-L again [Jérôme Hénin]
c050ce0 2017-09-18 Silence compiler warnings, remove Tabs [Giacomo Fiorin]
cb41905 2017-01-11 Add base class for TI estimator in other biases than ABF [Giacomo Fiorin]
a1bc676 2017-09-14 Avoid writing to unopened traj file [Jérôme Hénin]
b58d8cd 2017-09-08 Function to check for overlapping groups [Jérôme Hénin]
1e5efec 2017-09-07 Check for overlapping groups in coordNum [Jérôme Hénin]
03a61a4 2017-04-06 Add UI-based estimator [fhh2626]
ae43754 2017-08-17 Fix outputCenters parsing [Josh Vermaas]
1619e0e 2017-08-14 Delete static feature arrays in cvm destructor [Jérôme Hénin]

lib/colvars/colvarproxy.cpp

@@ -10,6 +10,10 @@
 #include <sstream>
 #include <string.h>
 
+#if defined(_OPENMP)
+#include <omp.h>
+#endif
+
 #include "colvarmodule.h"
 #include "colvarproxy.h"
 #include "colvarscript.h"
@@ -40,6 +44,12 @@ bool colvarproxy_system::total_forces_enabled() const
 }
 
 
+bool colvarproxy_system::total_forces_same_step() const
+{
+  return false;
+}
+
+
 cvm::real colvarproxy_system::position_dist2(cvm::atom_pos const &pos1,
                                              cvm::atom_pos const &pos2)
 {
@@ -204,7 +214,13 @@ void colvarproxy_atom_groups::clear_atom_group(int index)
 
 colvarproxy_smp::colvarproxy_smp()
 {
-  b_smp_active = true;
+  b_smp_active = true; // May be disabled by user option
+  omp_lock_state = NULL;
+#if defined(_OPENMP)
+  if (smp_thread_id() == 0) {
+    omp_init_lock(reinterpret_cast<omp_lock_t *>(omp_lock_state));
+  }
+#endif
 }
 
 
@@ -213,60 +229,143 @@ colvarproxy_smp::~colvarproxy_smp() {}
 
 int colvarproxy_smp::smp_enabled()
 {
+#if defined(_OPENMP)
+  if (b_smp_active) {
+    return COLVARS_OK;
+  }
+  return COLVARS_ERROR;
+#else
   return COLVARS_NOT_IMPLEMENTED;
+#endif
 }
 
 
 int colvarproxy_smp::smp_colvars_loop()
 {
+#if defined(_OPENMP)
+  colvarmodule *cv = cvm::main();
+  colvarproxy *proxy = cv->proxy;
+#pragma omp parallel for
+  for (size_t i = 0; i < cv->variables_active_smp()->size(); i++) {
+    colvar *x = (*(cv->variables_active_smp()))[i];
+    int x_item = (*(cv->variables_active_smp_items()))[i];
+    if (cvm::debug()) {
+      cvm::log("["+cvm::to_str(proxy->smp_thread_id())+"/"+
+               cvm::to_str(proxy->smp_num_threads())+
+               "]: calc_colvars_items_smp(), i = "+cvm::to_str(i)+", cv = "+
+               x->name+", cvc = "+cvm::to_str(x_item)+"\n");
+    }
+    x->calc_cvcs(x_item, 1);
+  }
+  return cvm::get_error();
+#else
   return COLVARS_NOT_IMPLEMENTED;
+#endif
 }
 
 
 int colvarproxy_smp::smp_biases_loop()
 {
+#if defined(_OPENMP)
+  colvarmodule *cv = cvm::main();
+#pragma omp parallel
+  {
+#pragma omp for
+    for (size_t i = 0; i < cv->biases_active()->size(); i++) {
+      colvarbias *b = (*(cv->biases_active()))[i];
+      if (cvm::debug()) {
+        cvm::log("Calculating bias \""+b->name+"\" on thread "+
+                 cvm::to_str(smp_thread_id())+"\n");
+      }
+      b->update();
+    }
+  }
+  return cvm::get_error();
+#else
   return COLVARS_NOT_IMPLEMENTED;
+#endif
 }
 
 
 int colvarproxy_smp::smp_biases_script_loop()
 {
+#if defined(_OPENMP)
+  colvarmodule *cv = cvm::main();
+#pragma omp parallel
+  {
+#pragma omp single nowait
+    {
+      cv->calc_scripted_forces();
+    }
+#pragma omp for
+    for (size_t i = 0; i < cv->biases_active()->size(); i++) {
+      colvarbias *b = (*(cv->biases_active()))[i];
+      if (cvm::debug()) {
+        cvm::log("Calculating bias \""+b->name+"\" on thread "+
+                 cvm::to_str(smp_thread_id())+"\n");
+      }
+      b->update();
+    }
+  }
+  return cvm::get_error();
+#else
   return COLVARS_NOT_IMPLEMENTED;
+#endif
 }
 
 
+
+
 int colvarproxy_smp::smp_thread_id()
 {
+#if defined(_OPENMP)
+  return omp_get_thread_num();
+#else
   return COLVARS_NOT_IMPLEMENTED;
+#endif
 }
 
 
 int colvarproxy_smp::smp_num_threads()
 {
+#if defined(_OPENMP)
+  return omp_get_max_threads();
+#else
   return COLVARS_NOT_IMPLEMENTED;
+#endif
 }
 
 
 int colvarproxy_smp::smp_lock()
 {
+#if defined(_OPENMP)
+  omp_set_lock(reinterpret_cast<omp_lock_t *>(omp_lock_state));
+#endif
   return COLVARS_OK;
 }
 
 
 int colvarproxy_smp::smp_trylock()
 {
+#if defined(_OPENMP)
+  return omp_test_lock(reinterpret_cast<omp_lock_t *>(omp_lock_state)) ?
+    COLVARS_OK : COLVARS_ERROR;
+#else
   return COLVARS_OK;
+#endif
 }
 
 
 int colvarproxy_smp::smp_unlock()
 {
+#if defined(_OPENMP)
+  omp_unset_lock(reinterpret_cast<omp_lock_t *>(omp_lock_state));
+#endif
   return COLVARS_OK;
 }
 
 
 
-
 colvarproxy_replicas::colvarproxy_replicas() {}