Update Colvars library to version 2020-01-27

One new feature (arithmetic path variables) and several smaller enhancements or bugfixes. Fix error check when loading an old state file https://github.com/Colvars/colvars/pull/317 Get default values for grid boundaries when available https://github.com/Colvars/colvars/pull/310 Allow redefining existing index groups (warn when this happens) https://github.com/Colvars/colvars/pull/302 Simplified replica communication syntax in metadynamics https://github.com/Colvars/colvars/pull/301 Obtain the bias_energy for ABF biases https://github.com/Colvars/colvars/pull/294 Fix reading path file with vector CVCs https://github.com/Colvars/colvars/pull/288 Fix segfault at deleting CVBasedPath https://github.com/Colvars/colvars/pull/286 Parrinello's (arithmetic) pathCV in CV space https://github.com/Colvars/colvars/pull/274 Fix race condition when starting a bundle of walkers https://github.com/Colvars/colvars/pull/279
2020-01-27 13:39:58 -05:00
parent 5eef3b1828
commit 9427fc50a5
56 changed files with 1876 additions and 1017 deletions
--- a/lib/colvars/colvarparams.cpp
+++ b/lib/colvars/colvarparams.cpp
@ -0,0 +1,111 @@
+// -*- c++ -*-
+
+// This file is part of the Collective Variables module (Colvars).
+// The original version of Colvars and its updates are located at:
+// https://github.com/Colvars/colvars
+// Please update all Colvars source files before making any changes.
+// If you wish to distribute your changes, please submit them to the
+// Colvars repository at GitHub.
+
+#include <sstream>
+#include <iostream>
+#include <algorithm>
+
+#include "colvarmodule.h"
+#include "colvarvalue.h"
+#include "colvarparams.h"
+
+
+
+colvarparams::colvarparams()
+{}
+
+
+colvarparams::~colvarparams()
+{}
+
+
+void colvarparams::register_param(std::string const &param_name,
+                                  void *param_ptr)
+{
+  param_map[param_name] = param_ptr;
+}
+
+
+void colvarparams::register_param_grad(std::string const &param_name,
+                                       colvarvalue *param_grad_ptr)
+{
+  param_grad_map[param_name] = param_grad_ptr;
+}
+
+
+int colvarparams::param_exists(std::string const &param_name)
+{
+  if (param_map.count(param_name) > 0) {
+    return COLVARS_OK;
+  }
+  return INPUT_ERROR;
+}
+
+
+std::vector<std::string> colvarparams::get_param_names()
+{
+  std::vector<std::string> result;
+  for (std::map<std::string, void const *>::const_iterator elem =
+         param_map.begin(); elem != param_map.end(); elem++) {
+    result.push_back(elem->first);
+  }
+  return result;
+}
+
+
+std::vector<std::string> colvarparams::get_param_grad_names()
+{
+  std::vector<std::string> result;
+  for (std::map<std::string, colvarvalue const *>::const_iterator elem =
+         param_grad_map.begin(); elem != param_grad_map.end(); elem++) {
+    result.push_back(elem->first);
+  }
+  return result;
+}
+
+
+void const *colvarparams::get_param_ptr(std::string const &param_name)
+{
+  if (param_map.count(param_name) > 0) {
+    return param_map[param_name];
+  }
+  cvm::error("Error: parameter \""+param_name+"\" not found.\n", INPUT_ERROR);
+  return NULL;
+}
+
+
+void const *colvarparams::get_param_grad_ptr(std::string const &param_name)
+{
+  if (param_grad_map.count(param_name) > 0) {
+    return param_grad_map[param_name];
+  }
+  cvm::error("Error: gradient of parameter \""+param_name+"\" not found.\n",
+             INPUT_ERROR);
+  return NULL;
+}
+
+
+cvm::real colvarparams::get_param(std::string const &param_name)
+{
+  cvm::real const *ptr =
+    reinterpret_cast<cvm::real const *>(get_param_ptr(param_name));
+  return ptr != NULL ? *ptr : 0.0;
+}
+
+
+int colvarparams::set_param(std::string const &param_name,
+                            void const *new_value)
+{
+  if (param_map.count(param_name) > 0) {
+    return cvm::error("Error: parameter \""+param_name+"\" cannot be "
+                      "modified.\n", COLVARS_NOT_IMPLEMENTED);
+  }
+  return cvm::error("Error: parameter \""+param_name+"\" not found.\n",
+                    INPUT_ERROR);
+}