refactor: completely remove static colvardeps

colvartools/poisson_integrator.cpp

@@ -17,14 +17,14 @@ int main (int argc, char *argv[]) {
   proxy->cvmodule = new colvarmodule(proxy); // This could be omitted if we used the colvarproxy_stub class
 
   std::string gradfile (argv[1]);
-  std::shared_ptr<colvar_grid_gradient> grad_ptr = std::make_shared<colvar_grid_gradient>(gradfile);
+  std::shared_ptr<colvar_grid_gradient> grad_ptr = std::make_shared<colvar_grid_gradient>(proxy->cvmodule, gradfile);
   if (proxy->cvmodule->get_error()) { return -1; }
 
   int itmax = 10000;
   cvm::real err;
   cvm::real tol = 1e-8;
 
-  colvargrid_integrate fes(grad_ptr);
+  colvargrid_integrate fes(proxy->cvmodule, grad_ptr);
   fes.set_div();
   fes.integrate(itmax, tol, err);
   fes.set_zero_minimum();

colvartools/poisson_integrator_conv.cpp

@@ -17,17 +17,17 @@ int main (int argc, char *argv[]) {
   proxy->cvmodule = new colvarmodule(proxy); // This could be omitted if we used the colvarproxy_stub class
 
   std::string gradfile (argv[1]);
-  std::shared_ptr<colvar_grid_gradient> grad_ptr = std::make_shared<colvar_grid_gradient>(gradfile);
+  std::shared_ptr<colvar_grid_gradient> grad_ptr = std::make_shared<colvar_grid_gradient>(proxy->cvmodule, gradfile);
   if (proxy->cvmodule->get_error()) { return -1; }
 
   cvm::real err = 1.;
   cvm::real tol = 1e-10;
 
-  colvargrid_integrate fes(grad_ptr);
+  colvargrid_integrate fes(proxy->cvmodule, grad_ptr);
   fes.set_div();
 
   // Load reference
-  colvar_grid_scalar ref(gradfile + ".ref");
+  colvar_grid_scalar ref(proxy->cvmodule, gradfile + ".ref");
   if (proxy->cvmodule->get_error()) { return -1; }
 
   if (ref.number_of_points() != fes.number_of_points()) {

lammps/src/COLVARS/colvarproxy_lammps.cpp

@@ -146,7 +146,7 @@ double colvarproxy_lammps::compute()
              (_lmp->domain->triclinic == 0)) {
     // Orthogonal unit cell
     boundaries_type = boundaries_pbc_ortho;
-    colvarproxy_system::update_pbc_lattice();
+    colvarproxy::update_pbc_lattice();
     // It is safer to let LAMMPS deal with high-tilt triclinic boxes
   } else {
     boundaries_type = boundaries_unsupported;

misc_interfaces/C_fortran/C_test.c

@@ -11,8 +11,8 @@ int main() {
 
     // Cannot yet call colvarscript without language interface
     unsigned char cmd[][256] = {"", "version" };
-    run_colvarscript_command(1, (unsigned char **)(cmd));
-    const char *res = get_colvarscript_result();
+    run_colvarscript_command(proxy, 1, (unsigned char **)(cmd));
+    const char *res = get_colvarscript_result(proxy);
     printf("Colvarscript claims it runs version %s\n", res);
     return 0;
 }

misc_interfaces/C_fortran/Makefile

@@ -7,7 +7,7 @@ COLVARS_LIB = ../../src/libcolvars.a
 COLVARS_SRC_DIR = ../../src
 IF_OBJ = colvarproxy_C.o
 
-CXXFLAGS := -std=c++11 -pedantic -g -O2 -fPIC
+CXXFLAGS := -std=c++17 -pedantic -g -O2 -fPIC
 
 .PHONY: default $(COLVARS_LIB)
 

misc_interfaces/C_fortran/colvarproxy_C.cpp

@@ -10,7 +10,7 @@ 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);
+    cvmodule = new colvarmodule(this);
     cvmodule->log("This is the Module speaking.");
 }
 

misc_interfaces/C_fortran/colvarproxy_C_interface.h

@@ -15,8 +15,8 @@ void call_proxy_member(void *proxy);
 // Functions of this type should define a complete interface
 // This could be based on colvarscript
 
-int run_colvarscript_command(int objc, unsigned char *const objv[]);
-const char * get_colvarscript_result();
+int run_colvarscript_command(void *proxy_in, int objc, unsigned char *const objv[]);
+const char * get_colvarscript_result(void *proxy_in);
 
 #ifdef __cplusplus
 }

namd/cudaglobalmaster/colvarproxy_cudaglobalmaster.C

@@ -175,7 +175,7 @@ public:
     return smp_mode_t::none;
   }
   std::vector<smp_mode_t> get_available_smp_modes() const override {
-    std::vector<colvarproxy_smp::smp_mode_t> available_modes{
+    std::vector<colvarproxy::smp_mode_t> available_modes{
       smp_mode_t::none,
       smp_mode_t::gpu
     };
@@ -351,9 +351,9 @@ void colvarproxy_impl::initialize_from_cudagm(
   if (simParams->firstTimestep != 0) {
     cvmodule->set_initial_step(static_cast<cvm::step_number>(simParams->firstTimestep));
   }
-  colvarproxy_io::set_output_prefix(std::string(simParams->outputFilename));
-  colvarproxy_io::set_restart_output_prefix(std::string(simParams->restartFilename));
-  colvarproxy_io::set_default_restart_frequency(simParams->restartFrequency);
+  colvarproxy::set_output_prefix(std::string(simParams->outputFilename));
+  colvarproxy::set_restart_output_prefix(std::string(simParams->restartFilename));
+  colvarproxy::set_default_restart_frequency(simParams->restartFrequency);
 }
 
 // Copied from colvarproxy_namd.C
@@ -814,9 +814,9 @@ void colvarproxy_impl::calculate() {
       // aware of this via the following flag
       b_simulation_continuing = true;
       // Update NAMD output and restart prefixes
-      colvarproxy_io::set_output_prefix(std::string(simParams->outputFilename));
-      colvarproxy_io::set_restart_output_prefix(std::string(simParams->restartFilename));
-      colvarproxy_io::set_default_restart_frequency(simParams->restartFrequency);
+      colvarproxy::set_output_prefix(std::string(simParams->outputFilename));
+      colvarproxy::set_restart_output_prefix(std::string(simParams->restartFilename));
+      colvarproxy::set_default_restart_frequency(simParams->restartFrequency);
       cvmodule->setup_output();
     }
   }
@@ -1018,7 +1018,7 @@ void colvarproxy_impl::set_lattice() {
     } else {
       boundaries_type = boundaries_pbc_triclinic;
     }
-    colvarproxy_system::update_pbc_lattice();
+    colvarproxy::update_pbc_lattice();
   } else {
     boundaries_type = boundaries_unsupported;
   }

namd/src/colvarproxy_namd.C

@@ -82,7 +82,7 @@ colvarproxy_namd::colvarproxy_namd(GlobalMasterColvars *gm)
 
   // find the input state file
   StringList *input_restart = Node::Object()->configList->find("colvarsInput");
-  colvarproxy_io::set_input_prefix(input_restart ? input_restart->data : "");
+  colvarproxy::set_input_prefix(input_restart ? input_restart->data : "");
 
   update_target_temperature();
   set_integration_timestep(simparams->dt);
@@ -94,9 +94,9 @@ colvarproxy_namd::colvarproxy_namd(GlobalMasterColvars *gm)
   updated_masses_ = updated_charges_ = true;
 
   // Take the output prefixes from the NAMD input
-  colvarproxy_io::set_output_prefix(std::string(simparams->outputFilename));
-  colvarproxy_io::set_restart_output_prefix(std::string(simparams->restartFilename));
-  colvarproxy_io::set_default_restart_frequency(simparams->restartFrequency);
+  colvarproxy::set_output_prefix(std::string(simparams->outputFilename));
+  colvarproxy::set_restart_output_prefix(std::string(simparams->restartFilename));
+  colvarproxy::set_default_restart_frequency(simparams->restartFrequency);
 
   if (simparams->accelMDOn) {
     accelMDOn = true;
@@ -376,9 +376,9 @@ void colvarproxy_namd::calculate()
       b_simulation_continuing = true;
 
       // Update NAMD output and restart prefixes
-      colvarproxy_io::set_output_prefix(std::string(simparams->outputFilename));
-      colvarproxy_io::set_restart_output_prefix(std::string(simparams->restartFilename));
-      colvarproxy_io::set_default_restart_frequency(simparams->restartFrequency);
+      colvarproxy::set_output_prefix(std::string(simparams->outputFilename));
+      colvarproxy::set_restart_output_prefix(std::string(simparams->restartFilename));
+      colvarproxy::set_default_restart_frequency(simparams->restartFrequency);
       cvmodule->setup_output();
 
     }
@@ -407,7 +407,7 @@ void colvarproxy_namd::calculate()
     } else {
       boundaries_type = boundaries_pbc_triclinic;
     }
-    colvarproxy_system::update_pbc_lattice();
+    colvarproxy::update_pbc_lattice();
   } else {
     boundaries_type = boundaries_unsupported;
   }

namd/src/colvarproxy_namd.h

@@ -128,7 +128,7 @@ class colvarproxy_namd : public colvarproxy {
     return smp_mode_t::cvcs;
   }
   std::vector<smp_mode_t> get_available_smp_modes() const override {
-    std::vector<colvarproxy_smp::smp_mode_t> available_modes{
+    std::vector<colvarproxy::smp_mode_t> available_modes{
       smp_mode_t::cvcs,
       smp_mode_t::inner_loop,
       smp_mode_t::none

src/Makefile

@@ -17,7 +17,7 @@ ifeq ($(CXX),)
 CXX := g++
 endif
 ifeq ($(CXXFLAGS),)
-CXXFLAGS := -std=c++11 -pedantic -g -O2 -fPIC
+CXXFLAGS := -std=c++17 -pedantic -g -O2 -fPIC
 ifneq ($(CXX),"CC")
 CXXFLAGS += -Wall
 endif

src/colvar.cpp

@@ -23,8 +23,8 @@
 #include "colvarcomp_torchann.h"
 #include "colvarcomp_coordnums.h"
 
-std::map<std::string, std::function<colvar::cvc *()>> colvar::global_cvc_map =
-    std::map<std::string, std::function<colvar::cvc *()>>();
+std::map<std::string, std::function<colvar::cvc *(colvarmodule *cvmodule_in)>> colvar::global_cvc_map =
+    std::map<std::string, std::function<colvar::cvc *(colvarmodule *cvmodule_in)>>();
 
 std::map<std::string, std::string> colvar::global_cvc_desc_map =
     std::map<std::string, std::string>();
@@ -822,8 +822,8 @@ template <typename def_class_name>
 void colvar::add_component_type(char const *def_description, char const *def_config_key)
 {
   if (global_cvc_map.count(def_config_key) == 0) {
-    global_cvc_map[def_config_key] = []() {
-      return new def_class_name();
+    global_cvc_map[def_config_key] = [](colvarmodule *cvmodule_in) {
+      return new def_class_name(cvmodule_in);
     };
     global_cvc_desc_map[def_config_key] = std::string(def_description);
   }
@@ -845,7 +845,7 @@ int colvar::init_components_type(const std::string& conf, const char* def_config
              "a new \""+std::string(def_config_key)+"\" component"+
              (cvm::debug() ? ", with configuration:\n"+def_conf
               : ".\n"));
-    cvc *cvcp = global_cvc_map[def_config_key]();
+    cvc *cvcp = global_cvc_map[def_config_key](cvmodule);
     if (!cvcp) {
       return cvmodule->error("Error: in creating object of type \"" + std::string(def_config_key) +
                             "\".\n",
@@ -1991,7 +1991,7 @@ void colvar::update_extended_Lagrangian()
   // [O] leap to v_(i+1/2) (10c)
   if (is_enabled(f_cv_Langevin)) {
     colvarvalue rnd(x);
-    rnd.set_random();
+    rnd.set_random(this->cvmodule);
     // ext_sigma has been computed at init time according to (10c)
     v_ext = cvm::exp(- 1.0 * dt * ext_gamma) * v_ext + ext_sigma * rnd / ext_mass;
   }

src/colvar.h

@@ -652,7 +652,7 @@ class colvar : public colvardeps {
   class map_total;
 
   /// A global mapping of cvc names to the cvc constructors
-  static const std::map<std::string, std::function<colvar::cvc *()>> &get_global_cvc_map()
+  static const std::map<std::string, std::function<colvar::cvc *(colvarmodule *cvmodule_in)>> &get_global_cvc_map()
   {
     return global_cvc_map;
   }
@@ -705,7 +705,7 @@ class colvar : public colvardeps {
 #endif
 
   /// A global mapping of cvc names to the cvc constructors
-  static std::map<std::string, std::function<colvar::cvc *()>> global_cvc_map;
+  static std::map<std::string, std::function<colvar::cvc *(colvarmodule *cvmodule_in)>> global_cvc_map;
 
   /// A global mapping of cvc names to the corresponding descriptions
   static std::map<std::string, std::string> global_cvc_desc_map;