CMake and some interface stuff

CMakeLists.txt

@@ -0,0 +1,92 @@
+cmake_minimum_required(VERSION 3.18)
+project(cpp-d4)
+set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
+
+if(NOT DEFINED D4LIBS_DIR AND NOT DEFINED D4INCLUDE_DIR)
+  	find_package(LAPACKE REQUIRED)
+	find_package(CBLAS CONFIG REQUIRED)
+endif(NOT DEFINED D4LIBS_DIR AND NOT DEFINED D4INCLUDE_DIR)
+
+
+IF(CMAKE_COMPILER_IS_GNUCXX)
+    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-reorder -pedantic \
+                                           -Wextra -Wcast-align -Wcast-qual  -Wchar-subscripts  \
+                                           -Wcomment -Wdisabled-optimization \
+                                           -Wformat  -Wformat=2 -Wformat-nonliteral -Wformat-security\
+                                           -Wformat-y2k  -Wimport  -Winit-self  -Winline -Winvalid-pch\
+                                           -Wunsafe-loop-optimizations  -Wmissing-braces\
+                                           -Wmissing-field-initializers -Wmissing-format-attribute  \
+                                           -Wmissing-include-dirs -Wmissing-noreturn -Wpacked  -Wparentheses\
+                                           -Wpointer-arith -Wredundant-decls -Wsequence-point\
+                                           -Wsign-compare  -Wstack-protector -Wstrict-aliasing\
+                                           -Wstrict-aliasing=2 -Wswitch -Wsuggest-override\
+                                           -Wtrigraphs  -Wuninitialized -Wunknown-pragmas  -Wunreachable-code\
+                                           -Wunused -Wunused-function  -Wunused-label  -Wunused-parameter\
+                                           -Wunused-value  -Wunused-variable  -Wvariadic-macros\
+                                           -Wvolatile-register-var  -Wwrite-strings -Wdeprecated-declarations\
+                                           -Wno-error=unused-local-typedefs -Wno-error=enum-compare -Wno-narrowing -Werror=return-type -g")
+set (GCC ON)
+if(WIN32) # Check if we are on Windows
+else()
+    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -rdynamic")
+endif(WIN32)
+ENDIF(CMAKE_COMPILER_IS_GNUCXX)
+
+include_directories(${PROJECT_SOURCE_DIR}/include ${PROJECT_BINARY_DIR} )
+if(DEFINED D4LIBS_DIR AND DEFINED D4INCLUDE_DIR)
+	include_directories(${D4INCLUDE_DIR})
+endif(DEFINED D4LIBS_DIR AND DEFINED D4INCLUDE_DIR)
+
+
+set(cpp_d4_SRC
+  src/damping/atm.cpp
+  src/damping/rational.cpp
+  src/dftd_cutoff.cpp
+  src/dftd_damping.cpp
+  src/dftd_dispersion.cpp
+  src/dftd_eeq.cpp 
+  src/dftd_model.cpp
+  src/dftd_ncoord.cpp
+  src/dftd_readxyz.cpp
+  )
+
+add_library(libcpp_d4  ${cpp_d4_SRC})
+
+add_executable(cpp-d4
+  src/program_dftd.cpp
+)
+
+add_executable(cpp-d4_test
+  test/main.cpp
+  test/test_grad.cpp
+  test/molecules.cpp
+  test/test_disp.cpp
+  test/test_disp2.cpp
+  test/test_ncoord.cpp
+  test/test_param.cpp
+  test/util.cpp
+)
+
+if(DEFINED D4LIBS_DIR AND DEFINED D4INCLUDE_DIR)
+	link_directories(${D4LIBS_DIR})
+
+	target_link_libraries(cpp-d4 libcpp_d4 cblas  lapacke pthread)
+	target_link_libraries(cpp-d4_test libcpp_d4 cblas lapacke pthread)
+else()
+	target_link_libraries(cpp-d4 libcpp_d4 ${LAPACKE_LIBRARIES}  ${CBLAS_LIBRARIES} pthread)
+	target_link_libraries(cpp-d4_test libcpp_d4 ${LAPACKE_LIBRARIES}  ${CBLAS_LIBRARIES} pthread)
+endif(DEFINED D4LIBS_DIR AND DEFINED D4INCLUDE_DIR)
+
+include(CTest)
+
+add_test(NAME disp2 COMMAND cpp-d4_test disp)
+add_test(NAME disp COMMAND cpp-d4_test disp)
+add_test(NAME grad COMMAND cpp-d4_test grad)
+add_test(NAME ncoord COMMAND cpp-d4_test ncoord)
+add_test(NAME param COMMAND cpp-d4_test param)
+
+
+if(WIN32) # Check if we are on Windows
+else()
+     target_link_libraries(cpp-d4 dl )
+endif(WIN32)

README.md

@@ -6,8 +6,11 @@
 This project is a port of the [`dftd4`](https://github.com/dftd4/dftd4) project
 to C++ and provides the D4(EEQ)-ATM method.
 
-## Building This Project
+## Requirements
+cpp-d4 depends on cblas and lapacke, the C implementation of blas and lapack.
+
 
+## Building This Project
 This project is build with `meson`, to setup and perform a build run:
 
 ```bash
@@ -21,6 +24,45 @@ Run the test suite with:
 meson test -C _build --print-errorlogs
 ```
 
+In addition to `meson`, one can use CMake to build cpp-d4 and include it into external projects (see for example [https://github.com/conradhuebler/curcuma](https://github.com/conradhuebler/curcuma)). 
+
+```bash
+cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo ..
+make
+```
+The tests can be started with
+
+```bash
+make test
+```
+In case, cblas and lapacke can not be found using cmake (which for example happens on Ubuntu), one can specify one include and library path for both dependencies.
+
+```bash
+cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo .. -DD4LIBS_DIR=/usr/lib/ -DD4INCLUDE_DIR=/usr/include/
+```
+
+```bash
+cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo .. -DD4LIBS_DIR=$(find /usr -name 'cblas.so' |head -n1 |sed 's/cblas.so//g') -DD4INCLUDE_DIR=$(find /usr -name 'cblas.h' |head -n1 |sed 's/cblas.h//g')
+```
+
+Using CMake it is then easy to include cpp-d4 in an own project.
+
+```cmake
+if(NOT DEFINED D4LIBS_DIR AND NOT DEFINED D4INCLUDE_DIR)
+  	find_package(LAPACKE REQUIRED)
+	find_package(CBLAS CONFIG REQUIRED)
+else()
+	include_directories(${INCLUDE_DIR})
+endif(DEFINED D4LIBS_DIR AND DEFINED D4INCLUDE_DIR)
+
+add_subdirectory(cpp-d4)
+
+if(DEFINED D4LIBS_DIR AND DEFINED D4INCLUDE_DIR)
+    target_link_libraries(yourproject PUBLIC libcpp_d4 cblas lapacke )
+else()
+    target_link_libraries(yourproject PUBLIC libcpp_d4 ${LAPACKE_LIBRARIES}  ${CBLAS_LIBRARIES} )
+endif(DEFINED D4LIBS_DIR AND DEFINED D4INCLUDE_DIR)
+```
 ## Citations
 
 - E. Caldeweyher, C. Bannwarth and S. Grimme, _J. Chem. Phys._, **2017**, 147, 034112. DOI: [10.1063/1.4993215](https://dx.doi.org/10.1063/1.4993215)

include/dftd_geometry.h

@@ -42,6 +42,52 @@ class TMolecule {
     xyz.Delete();
     at.Delete();
   }
+
+  /* set structure by array of coords (double), atom types (int) and number of atoms */
+  /* Geometry has to be in bohrs */
+  void SetGeometry(const double* coord, const int* attype, int number)
+  {
+      GetMemory(number);
+      for(int i = 0; i < NAtoms; ++i)
+      {
+          at(i) = attype[i];
+          xyz(i, 0) = coord[3*i + 0];
+          xyz(i, 1) = coord[3*i + 1];
+          xyz(i, 2) = coord[3*i + 2];
+      }
+  }
+
+  /* update the geometry */
+  /* Geometry has to be in bohrs */
+  void UpdateGeometry(const double* coord)
+  {
+      for(int i = 0; i < NAtoms; ++i)
+      {
+          xyz(i, 0) = coord[3*i + 0];
+          xyz(i, 1) = coord[3*i + 1];
+          xyz(i, 2) = coord[3*i + 2];
+      }
+  }
+
+  /* update the position of a single atom (index, coord and element) */
+  /* Geometry has to be in bohrs */
+  void UpdateAtom(int index, double x, double y, double z, int element = -1)
+  {
+      //std::cout << x << " " << y << " " << z << std::endl;
+      if(element != -1)
+        at(index) = element;
+      xyz(index, 0) = x;
+      xyz(index, 1) = y;
+      xyz(index, 2) = z;
+  }
+
+  void Print() const
+  {
+      for(int i = 0; i < NAtoms; ++i)
+      {
+          std::cout << at(i) << " " << xyz(i, 0) << " " << xyz(i, 1) << " " << xyz(i, 2) << std::endl;
+      }
+  }
 };
 
 } // namespace dftd4