Fix segfault in NAMD

colvartools/poisson_integrator.cpp

@@ -14,7 +14,8 @@ int main (int argc, char *argv[]) {
   }
 
   colvarproxy *proxy = new colvarproxy();
-  proxy->colvars = new colvarmodule(proxy); // This could be omitted if we used the colvarproxy_stub class
+  proxy->colvars = new colvarmodule(); // This could be omitted if we used the colvarproxy_stub class
+  proxy->colvars->init(proxy);
 
   std::string gradfile (argv[1]);
   std::shared_ptr<colvar_grid_gradient> grad_ptr = std::make_shared<colvar_grid_gradient>(gradfile);

colvartools/poisson_integrator_conv.cpp

@@ -14,7 +14,8 @@ int main (int argc, char *argv[]) {
   }
 
   colvarproxy *proxy = new colvarproxy();
-  proxy->colvars = new colvarmodule(proxy); // This could be omitted if we used the colvarproxy_stub class
+  proxy->colvars = new colvarmodule(); // This could be omitted if we used the colvarproxy_stub class
+  proxy->colvars->init(proxy);
 
   std::string gradfile (argv[1]);
   std::shared_ptr<colvar_grid_gradient> grad_ptr = std::make_shared<colvar_grid_gradient>(gradfile);

gromacs/src/applied_forces/colvars/colvarproxygromacs.cpp.patch

@@ -0,0 +1,24 @@
+diff --git a/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp b/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp
+index 76b350c611..e0eaedfd61 100644
+--- a/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp
++++ b/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp
+@@ -79,9 +79,6 @@ ColvarProxyGromacs::ColvarProxyGromacs(const std::string& colvarsConfigString,
+     // Retrieve masses and charges from input file
+     updated_masses_ = updated_charges_ = true;
+
+-    // User-scripted forces are not available in GROMACS
+-    have_scripts = false;
+-
+     angstrom_value_ = 0.1;
+
+     // From Gnu units
+@@ -117,7 +114,8 @@ ColvarProxyGromacs::ColvarProxyGromacs(const std::string& colvarsConfigString,
+             input_streams_[inputName] = new std::istringstream(content);
+         }
+
+-        colvars = new colvarmodule(this);
++        colvars = new colvarmodule();
++        colvars->init(this);
+         cvm::log(cvm::line_marker);
+         cvm::log("Start colvars Initialization.");
+

lammps/src/COLVARS/colvarproxy_lammps.cpp

@@ -46,7 +46,8 @@ void colvarproxy_lammps::init()
   version_int = get_version_from_string(COLVARPROXY_VERSION);
 
   // create the colvarmodule instance
-  colvars = new colvarmodule(this);
+  colvars = new colvarmodule();
+  colvars->init(this);
 
   // Create instance of scripting interface
   script = new colvarscript(this, colvars);

misc_interfaces/C_fortran/colvarproxy_C.cpp

@@ -10,7 +10,8 @@ static colvarproxy* unique_colvarproxy_object;
 colvarproxy_C::colvarproxy_C()
 {
     std::cerr << "This is the colvarproxy_C constructor at address " << this << std::endl;
-    colvars = new colvarmodule(this);
+    colvars = new colvarmodule();
+    colvars->init(this);
     colvars->log("This is the Module speaking.");
 }
 

misc_interfaces/stubs/colvarproxy_stub.cpp

@@ -29,7 +29,8 @@ colvarproxy_stub::colvarproxy_stub()
   // both fields are taken from data structures already available
   updated_masses_ = updated_charges_ = true;
 
-  colvars = new colvarmodule(this);
+  colvars = new colvarmodule();
+  colvars->init(this);
   cvm::log("Using minimal testing interface.\n");
 
   colvars->cv_traj_freq = 0; // I/O will be handled explicitly

namd/src/ComputeMgr.C.patch

@@ -0,0 +1,18 @@
+diff --git a/src/ComputeMgr.C b/src/ComputeMgr.C
+index 96cbb387..343111b5 100644
+--- a/src/ComputeMgr.C
++++ b/src/ComputeMgr.C
+@@ -1082,8 +1082,11 @@ ComputeMgr::createComputes(ComputeMap *map)
+             masterServerObject->addClient(new GlobalMasterMisc());
+         if ( simParams->freeEnergyOn )
+             masterServerObject->addClient(new GlobalMasterFreeEnergy());
+-	if ( simParams->colvarsOn )
+-	    masterServerObject->addClient(new GlobalMasterColvars());
++	if ( simParams->colvarsOn ) {
++          auto *m = new GlobalMasterColvars();
++          masterServerObject->addClient(m);
++          m->init();
++        }
+
+     }
+

namd/src/GlobalMaster.h.patch

@@ -0,0 +1,13 @@
+diff --git a/src/GlobalMaster.h b/src/GlobalMaster.h
+index bb27f2ee..373913c5 100644
+--- a/src/GlobalMaster.h
++++ b/src/GlobalMaster.h
+@@ -81,6 +81,8 @@ class GlobalMaster {
+  protected:
+   GlobalMaster();
+
++  virtual void init() {}
++
+   /* This will be called after the pointers to lists below have been
+      initialized correctly by processData.  It should perform any
+      required caluation and update the atom/force lists. */

namd/src/GlobalMasterColvars.C

@@ -5,7 +5,13 @@
 #include "colvarproxy_namd.h"
 
 
-GlobalMasterColvars::GlobalMasterColvars() : proxy(new colvarproxy_namd(this)) {}
+GlobalMasterColvars::GlobalMasterColvars() {}
+
+void GlobalMasterColvars::init()
+{
+  proxy.reset(new colvarproxy_namd());
+  proxy->init(this);
+}
 
 GlobalMasterColvars::~GlobalMasterColvars() { reset(); }
 

namd/src/GlobalMasterColvars.h

@@ -15,6 +15,8 @@ class GlobalMasterColvars : public GlobalMaster {
 
   ~GlobalMasterColvars();
 
+  void init() override;
+
   void reset();
 
   void calculate() override;

namd/src/colvarproxy_namd.C

@@ -46,8 +46,7 @@
 #include "colvarproxy_namd_version.h"
 
 
-colvarproxy_namd::colvarproxy_namd(GlobalMasterColvars *gm)
-  : globalmaster(gm)
+colvarproxy_namd::colvarproxy_namd()
 {
   engine_name_ = "NAMD";
 #if CMK_SMP && USE_CKLOOP
@@ -63,7 +62,6 @@ colvarproxy_namd::colvarproxy_namd(GlobalMasterColvars *gm)
   }
 #endif
   first_timestep = true;
-  globalmaster->requestTotalForcePublic(total_force_requested);
 
   boltzmann_ = 0.001987191;
 
@@ -75,9 +73,6 @@ colvarproxy_namd::colvarproxy_namd(GlobalMasterColvars *gm)
   if (cvm::debug())
     iout << "Info: initializing the colvars proxy object.\n" << endi;
 
-  // find the configuration file, if provided
-  StringList *config = Node::Object()->configList->find("colvarsConfig");
-
   // find the input state file
   StringList *input_restart = Node::Object()->configList->find("colvarsInput");
   colvarproxy_io::set_input_prefix(input_restart ? input_restart->data : "");
@@ -110,15 +105,25 @@ colvarproxy_namd::colvarproxy_namd(GlobalMasterColvars *gm)
   }
 
   init_atoms_map();
+}
+
+
+int colvarproxy_namd::init(GlobalMasterColvars *gm)
+{
+  globalmaster = gm;
 
   // initialize module: this object will be the communication proxy
-  colvars = new colvarmodule(this);
+  colvars = new colvarmodule();
+  colvars->init(this);
 
   cvm::log("Using NAMD interface, version "+
            cvm::to_str(COLVARPROXY_VERSION)+".\n");
   colvars->cite_feature("NAMD engine");
   colvars->cite_feature("Colvars-NAMD interface");
 
+  // find the configuration file, if provided
+  StringList *config = Node::Object()->configList->find("colvarsConfig");
+
   errno = 0;
   for ( ; config; config = config->next ) {
     add_config("configfile", config->data);
@@ -134,12 +139,6 @@ colvarproxy_namd::colvarproxy_namd(GlobalMasterColvars *gm)
   // save to Node for Tcl script access
   Node::Object()->colvars = colvars;
 
-#ifdef NAMD_TCL
-  have_scripts = true;
-#else
-  have_scripts = false;
-#endif
-
   if (simparams->firstTimestep != 0) {
     colvars->set_initial_step(static_cast<cvm::step_number>(simparams->firstTimestep));
   }
@@ -156,6 +155,8 @@ colvarproxy_namd::colvarproxy_namd(GlobalMasterColvars *gm)
 
   if (cvm::debug())
     iout << "Info: done initializing the colvars proxy object.\n" << endi;
+
+  return COLVARS_OK;
 }
 
 

namd/src/colvarproxy_namd.h

@@ -71,10 +71,14 @@ class colvarproxy_namd : public colvarproxy {
 
   void init_tcl_pointers() override;
 
-  colvarproxy_namd(GlobalMasterColvars *gm);
+  colvarproxy_namd();
   ~colvarproxy_namd();
 
+  /// Initialize Colvars module and interface with GlobalMaster
+  int init(GlobalMasterColvars *gm);
+
   int setup() override;
+
   int reset() override;
 
   /// Get the target temperature from the NAMD thermostats supported so far

src/colvarmodule.cpp

@@ -94,7 +94,7 @@ namespace {
 }
 
 
-colvarmodule::colvarmodule(colvarproxy *proxy_in)
+colvarmodule::colvarmodule()
 {
   depth_s = 0;
   log_level_ = 10;
@@ -109,8 +109,12 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
 
   usage_ = new usage();
   usage_->cite_feature("Colvars module");
+}
+
 
-  if (proxy != NULL) {
+void colvarmodule::init(colvarproxy *proxy_in)
+{
+  if (proxy) {
     // TODO relax this error to handle multiple molecules in VMD
     // once the module is not static anymore
     cvm::error("Error: trying to allocate the collective "

src/colvarmodule.h

@@ -370,14 +370,12 @@ static inline real acos(real const &x)
   size_t size() const;
 
   /// Constructor
-  /// \param Pointer to instance of the proxy class (communicate with engine)
-  colvarmodule(colvarproxy *proxy);
-
-private:
-
-  /// Cannot initialize the main object without a proxy
   colvarmodule();
 
+  /// Initialize interface with proxy and other complex objects
+  /// \param Pointer to instance of the proxy class (communicate with engine)
+  void init(colvarproxy *proxy);
+
 public:
 
   /// Destructor

src/colvarproxy.cpp

@@ -416,18 +416,14 @@ int colvarproxy_smp::smp_unlock()
 
 
 
-colvarproxy_script::colvarproxy_script()
-{
-  script = NULL;
-  have_scripts = false;
-}
+colvarproxy_script::colvarproxy_script() {}
 
 
 colvarproxy_script::~colvarproxy_script()
 {
-  if (script != NULL) {
+  if (script) {
     delete script;
-    script = NULL;
+    script = nullptr;
   }
 }
 

src/colvarproxy.h

@@ -529,10 +529,7 @@ class colvarproxy_script {
 
   /// Pointer to the scripting interface object
   /// (does not need to be allocated in a new interface)
-  colvarscript *script;
-
-  /// Do we have a scripting interface?
-  bool have_scripts;
+  colvarscript *script = nullptr;
 
   /// Run a user-defined colvar forces script
   virtual int run_force_callback();

src/colvarscript.cpp

@@ -649,7 +649,8 @@ int tcl_colvars_vmd_init(Tcl_Interp *interp, int molid);
 extern "C" {
   int Colvars_Init(Tcl_Interp *interp) {
     colvarproxy *proxy = new colvarproxy();
-    colvarmodule *colvars = new colvarmodule(proxy);
+    colvarmodule *colvars = new colvarmodule();
+    colvars->init(proxy);
     proxy->set_tcl_interp(interp);
     proxy->colvars = colvars;
     Tcl_CreateObjCommand(interp, "cv", tcl_run_colvarscript_command,

tests/functional_gpu/run_colvars_test_cuda.cpp

@@ -55,7 +55,8 @@ class colvarproxy_stub_gpu : public colvarproxy {
     return COLVARS_NOT_IMPLEMENTED;
   }
   void init_cvm() {
-    colvars = new colvarmodule(this);
+    colvars = new colvarmodule();
+    colvars->init(this);
     cvm::log("Using minimal CUDA testing interface.\n");
 
     colvars->cv_traj_freq = 0; // I/O will be handled explicitly

tests/unittests/embedded_tcl.cpp

@@ -8,7 +8,8 @@
 int main(int argc, char *argv[]) {
 
   colvarproxy *proxy = new colvarproxy();
-  proxy->colvars = new colvarmodule(proxy);
+  proxy->colvars = new colvarmodule();
+  proxy->colvars->init(proxy);
 
   int res = proxy->tcl_run_script("puts \"\n(Tcl) Tcl script running successfully using embedded interpreter.\"");
 

tests/unittests/file_io.cpp

@@ -8,7 +8,8 @@
 int main(int argc, char *argv[]) {
 
   colvarproxy *proxy = new colvarproxy();
-  proxy->colvars = new colvarmodule(proxy);
+  proxy->colvars = new colvarmodule();
+  proxy->colvars->init(proxy);
 
   proxy->backup_file("nonexistent.txt");
   proxy->remove_file("nonexistent.txt");

vmd/src/colvarproxy_vmd.C

@@ -85,18 +85,14 @@ colvarproxy_vmd::colvarproxy_vmd(Tcl_Interp *interp, VMDApp *v, int molid)
   // both fields are taken from data structures already available
   updated_masses_ = updated_charges_ = true;
 
-  // Do we have scripts?
-  // For now colvars depend on Tcl, but this may not always be the case
-  // in the future
 #if defined(VMDTCL)
-  have_scripts = true;
   // Need to set this before constructing colvarmodule, which creates colvarscript object
   set_tcl_interp(interp);
-#else
-  have_scripts = false;
 #endif
 
-  colvars = new colvarmodule(this);
+  colvars = new colvarmodule();
+  colvars->init(this);
+
   cvm::log("Using VMD interface, version "+
            cvm::to_str(COLVARPROXY_VERSION)+".\n");