Initial transfer of program-independent code from SVN r221

Also adds .gitignore

Author: berquist

.gitignore

@@ -0,0 +1,141 @@
+## C++
+
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+## Python
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+.static_storage/
+.media/
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/

CMakeLists.txt

@@ -0,0 +1,26 @@
+cmake_minimum_required(VERSION 2.8.5)
+project(LIBRESPONSE CXX)
+
+find_package(Armadillo REQUIRED)
+
+set(SRC
+    configurable.C
+    dump_ao_integrals.C
+    index_printing.C
+    indices.C
+    matvec_i.C
+    utils.C
+    linear/helpers.C
+    linear/interface.C
+    linear/interface_nonorthogonal.C
+    linear/printing.C
+    operator_spec.C
+    set_defaults.C
+    )
+
+add_library(response ${SRC})
+target_link_libraries(response "${ARMADILLO_LIBRARIES}")
+
+if(OPENMP_FOUND)
+    set_target_properties(response PROPERTIES COMPILE_FLAGS "${OpenMP_CXX_FLAGS}")
+endif(OPENMP_FOUND)

configurable.C

@@ -0,0 +1,24 @@
+#include <iostream>
+#include "configurable.h"
+
+namespace libresponse {
+
+const std::string &configurable::get_param(const std::string &key) const {
+    ssmap_it_type i = m_params.find(key);
+    return i == m_params.end() ? m_empty : i->second;
+}
+
+void configurable::cfg(const std::string &key, const std::string &val) {
+    m_params[key] = val;
+}
+
+void configurable::dump_params() const {
+    for (ssmap_it_type iter = m_params.begin(); iter != m_params.end(); ++iter)
+        std::cout << "   " << iter->first << ": " << iter->second << std::endl;
+}
+
+bool configurable::has_param(const std::string &key) const {
+    return static_cast<bool>(m_params.count(key));
+}
+
+} // namespace libresponse

configurable.h

@@ -0,0 +1,91 @@
+#ifndef LIBRESPONSE_CONFIGURABLE_H_
+#define LIBRESPONSE_CONFIGURABLE_H_
+
+/*!
+ * @file
+ *
+ * Inheritable configuration by wrapping a string->string map.
+ */
+
+#include <cstdlib>
+#include <map>
+#include <sstream>
+#include <string>
+#include <stdexcept>
+
+typedef std::map< std::string, std::string > ssmap;
+typedef ssmap::const_iterator ssmap_it_type;
+
+namespace libresponse {
+
+/*!
+ * Inheritable configuration by wrapping a string->string map.
+ */
+class configurable {
+private:
+    ssmap m_params; //!< Key-value parameters
+    std::string m_empty; //!< Empty value
+
+public:
+    /*!
+     * Default constructor
+     */
+    configurable() { }
+
+    const std::string &get_param(const std::string &key) const;
+    void cfg(const std::string &key, const std::string &val);
+
+    template<typename T>
+    void get_param(const std::string &key, T &val) const;
+
+    template<typename T>
+    T get_param(const std::string &key) const;
+
+    template<typename T>
+    void cfg(const std::string &key, const T &val);
+
+    /*!
+     * Print all key-value pairs to stdout
+     */
+    void dump_params() const;
+
+    bool has_param(const std::string &key) const;
+};
+
+
+template<typename T>
+void configurable::cfg(const std::string &key, const T &val) {
+
+    std::ostringstream ss;
+    ss << val;
+    cfg(key, ss.str());
+}
+
+
+template<typename T>
+void configurable::get_param(const std::string &key, T &val) const {
+
+    const std::string &par = get_param(key);
+    if (!par.empty()) {
+        std::stringstream ss;
+        ss << par; ss >> val;
+    }
+}
+
+
+template<typename T>
+T configurable::get_param(const std::string &key) const {
+
+    if(m_params.count(key) == 0) {
+        throw std::logic_error(
+            "configurable::get_param(): no parameter with given name: " + key);
+    }
+
+    T t;
+    get_param(key, t);
+    return t;
+}
+
+} // namespace libresponse
+
+#endif // LIBRESPONSE_CONFIGURABLE_H_

constants.h

@@ -0,0 +1,23 @@
+#ifndef LIBRESPONSE_CONSTANTS_H_
+#define LIBRESPONSE_CONSTANTS_H_
+
+/*!
+ * @brief Physical constants from CODATA 2014.
+ *
+ * @file
+ */
+
+#include <armadillo>
+#include <set>
+#include <vector>
+
+namespace libresponse {
+namespace constant {
+
+const double fine_structure_constant = 7.2973525664e-3;
+const double alpha = fine_structure_constant;
+
+} // namespace constant
+} // namespace libresponse
+
+#endif // LIBRESPONSE_CONSTANTS_H_

dump_ao_integrals.C

@@ -0,0 +1,23 @@
+#include "dump_ao_integrals.h"
+
+template void dump_integrals(
+    const arma::mat& arma_integrals,
+    const std::string& integral_description,
+    const std::string& input_basename,
+    const std::string& integral_filename_ending);
+template void dump_integrals(
+    const arma::cube& arma_integrals,
+    const std::string& integral_description,
+    const std::string& input_basename,
+    const std::string& integral_filename_ending);
+
+void dump_ao_integrals(const std::vector<libresponse::operator_spec> &operators, const std::string &basename)
+{
+    for (size_t i = 0; i < operators.size(); i++) {
+        dump_integrals(
+            operators[i].integrals_ao,
+            operators[i].metadata.operator_label,
+            basename,
+            operators[i].metadata.operator_label + std::string(".dat"));
+    }
+}

dump_ao_integrals.h

@@ -0,0 +1,40 @@
+#ifndef LIBRESPONSE_DUMP_AO_INTEGRALS_H_
+#define LIBRESPONSE_DUMP_AO_INTEGRALS_H_
+
+#include "operator_spec.h"
+
+/*!
+ * @brief Write the contents of an Armadillo container (matrix, cube)
+ * to disk.
+ */
+template<typename T>
+void dump_integrals(
+    const T& arma_integrals,
+    const std::string& integral_description,
+    const std::string& input_basename,
+    const std::string& integral_filename_ending) {
+
+    const std::string integral_filename = \
+        input_basename + "." + integral_filename_ending;
+
+    std::cout                      \
+        << "  Dumping "            \
+        << integral_description    \
+        << " integrals to file: "  \
+        << integral_filename       \
+        << std::endl;
+
+    const bool res = arma_integrals.save(integral_filename, arma::arma_ascii);
+
+    if (!res) {
+        std::cout << "  Couldn't save integrals to file." << std::endl;
+        throw 1;
+    }
+
+    return;
+
+}
+
+void dump_ao_integrals(const std::vector<libresponse::operator_spec> &operators, const std::string &basename);
+
+#endif // LIBRESPONSE_DUMP_AO_INTEGRALS_H_