Merge pull request #20 from libefp2/lyuda_Jan6

Lyuda jan6

.gitignore

@@ -24,5 +24,7 @@
 /include/
 tags
 build*/
-cmake-build-debug/
+/installed/
+/cmake-build-debug/
 compilation.log
+

CMakeLists.txt

@@ -4,7 +4,23 @@ if (POLICY CMP0135)
 endif ()
 
 # extract project version from source
+
+if(NOT DEFINED torch_switch)
+    if(DEFINED ENV{TORCH_SWITCH})
+        set(torch_switch $ENV{TORCH_SWITCH})
+    else()
+        set(torch_switch OFF)
+    endif()
+endif()
+
+option(torch_switch "Enable Torch library integration" ${TORCH_SWITCH})
+
+if(torch_switch)
+    add_definitions(-DTORCH_SWITCH)
+endif()
+
 file(STRINGS "src/efp.h" _src_efp_h REGEX "LIBEFP_VERSION_STRING")
+
 if (${_src_efp_h} MATCHES "^#define LIBEFP_VERSION_STRING \"(.*)\"$")
     set(_libefp_VERSION ${CMAKE_MATCH_1})
 endif()
@@ -13,9 +29,17 @@ project(
   libefp
   # someday when Makefile dropped, configure efp.h.in from cmake
   VERSION ${_libefp_VERSION}
-  LANGUAGES C
+  LANGUAGES C CXX
   )
-set(libefp_AUTHORS "Ilya A. Kaliman, Lori A. Burns, Dmitry Morozov, Carlos H. Borca, Yen (Terri) Bui, Yongbin Kim, Lyudmila V. Slipchenko")
+
+#set(CMAKE_INSTALL_PREFIX "${PROJECT_SOURCE_DIR}/installed" CACHE PATH "Installation directory" FORCE)
+#set(CMAKE_INSTALL_PREFIX "${LIBEFP_DIR}" CACHE PATH "Installation directory")
+set(CMAKE_INSTALL_LIBDIR "lib")
+
+### LVS needs this on MacOS silicon
+set(CMAKE_CXX_STANDARD 17)
+
+set(libefp_AUTHORS "Ilya A. Kaliman, Lori A. Burns, Suranjan Paul, Dmitry Morozov, Carlos H. Borca, Yen (Terri) Bui, Yongbin Kim, Lyudmila V. Slipchenko")
 set(libefp_DESCRIPTION "Parallel implementation of the Effective Fragment Potential method")
 set(libefp_URL "https://github.com/libefp2/libefp")
 set(libefp_LICENSE "BSD 2-clause")
@@ -24,6 +48,7 @@ list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
 
 set(efp libefp)  # Namespace
 
+
 # TODO: Remove when requiring cmake >= 3.21  # from LecrisUT/CMake-Template
 if (NOT DEFINED ${efp}_IS_TOP_LEVEL)
     if (CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
@@ -54,7 +79,10 @@ option_with_default(BUILD_FPIC "Libraries will be compiled with position indepen
 if((${BUILD_SHARED_LIBS}) AND NOT ${BUILD_FPIC})
     message(FATAL_ERROR "BUILD_SHARED_LIBS ON and BUILD_FPIC OFF are incompatible, as shared library requires position independent code")
 endif()
-option_with_print(LIBEFP_ENABLE_OPENMP "Enable OpenMP parallelization. Psi4 wants OFF" OFF)
+
+### This option turns OPENMP ON and OFF!
+option_with_print(LIBEFP_ENABLE_OPENMP "Enable OpenMP parallelization. Psi4 wants OFF" ON)
+
 option_with_print(ENABLE_GENERIC "Enable mostly static linking in shared library" OFF)
 include(xhost)  # defines: option(ENABLE_XHOST "Enable processor-specific optimization" ON)
 option_with_print(FRAGLIB_UNDERSCORE_L "DEPRECATED: Installed fragment library has names ending in _L. Psi4 wants OFF" ON)
@@ -132,6 +160,7 @@ set(raw_sources_list
   util.c
   xr.c
   )
+
 set(src_prefix "src/")
 string(REGEX REPLACE "([^;]+)" "${src_prefix}\\1" sources_list "${raw_sources_list}")
 
@@ -203,6 +232,9 @@ install(FILES fraglib/makefp.inp
 install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/fraglib
         DESTINATION ${CMAKE_INSTALL_DATADIR}/${efp})
 
+install(DIRECTORY ${PROJECT_SOURCE_DIR}/nnlib
+        DESTINATION ${CMAKE_INSTALL_DATADIR}/${efp})
+
 # headers NOT namespace protected
 install(FILES ${src_prefix}/efp.h
         DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})

CONTRIBUTORS

@@ -1,10 +1,11 @@
 Libefp was written by Ilya Kaliman.
 The following people contributed to libefp. Thanks!
 
+Yen (Terri) Bui
 Lori A. Burns
-Dmitry Morozov
 Carlos H. Borca
-Yen (Terri) Bui
 Yongbin Kim
+Dmitry Morozov
+Suranjan Paul
 Lyudmila V. Slipchenko
 

Makefile

@@ -5,6 +5,7 @@ all: efpmd
 efpmd: libefp
 	cd efpmd/libff && CC="$(CC)" CFLAGS="$(MYCFLAGS)" $(MAKE)
 	cd efpmd/libopt && CC="$(CC)" CFLAGS="$(MYCFLAGS)" FC="$(FC)" FFLAGS="$(MYFFLAGS)" $(MAKE)
+	cd efpmd/torch && CC="$(CC)" CFLAGS="$(MYCFLAGS)" $(MAKE)
 	cd efpmd/src && $(MAKE)
 
 libefp:
@@ -15,6 +16,7 @@ clean:
 	cd tests && $(MAKE) $@
 	cd efpmd/libff && $(MAKE) $@
 	cd efpmd/libopt && $(MAKE) $@
+	cd efpmd/torch && $(MAKE) $@
 	cd efpmd/src && $(MAKE) $@
 	rm -rf doxygen_html
 

README-torch.md

@@ -0,0 +1,56 @@
+
+# Installation with LibTorch for ML/EFP models
+
+## Required libraries
+
+- cmake
+- lapack math library
+- C/C++ compiler (GCC 9 or newer)
+- Fortran 77 compiler 
+
+An example of working setup at Purdue supercomputers 
+can be foound in *module.sh* script. 
+
+AppleClang 14 works on M2 MacOS Ventura.   
+
+## LibTorch library
+
+For ML/EFP models, one needs to use LibTorch library. 
+Install LibTorch (C++ frontend) of PyTorch. Consult Libtorch/Pytorch 
+webpages for detail: https://pytorch.org/cppdocs/
+
+You can opt out and configure with EFP-only installation - see the next section.
+
+## Setup environmental variables
+
+*setup.sh* or *setup.csh* are used to set up environmental 
+variables. The first two are mandatory:
+
+`TORCH_SWITCH` is the variable governing compilation 
+with or without LibTorch.
+
+`LIBEFP_DIR` is a path to LibEFP directory with source codes. 
+
+`INSTALLATION_DIR` is the installation directory. 
+
+`TORCH_INSTALLED_DIR` and `LIBTORCH_INCLUDE_DIRS` are paths to the LibTorch 
+installation and included directories. 
+
+## Compilation 
+
+Further tuning can be done in `CMakeLists.txt`. Otherwise,
+run `./compile.sh` to compile.
+
+Executable `efpmd` will be in `build/efpmd/efpmd` and in 
+
+## Running test jobs
+
+Test jobs are contained in `tests` directory.To check the complilation, 
+do 
+
+`cd tests`
+
+`make check`
+
+This will run all the test jobs and report `SUCCESS/FAILURE`. Examine any failed jobs carefully.
+

README.md

@@ -27,6 +27,10 @@ The latest release can be downloaded
 
 ## Installation
 
+**See [README-torch.md](README-torch.md) for the up-to-date installation instructions!
+For additional CMake instructions, see [README-cmake.md](README-cmake.md).
+The section below is outdated.**
+
 To build LIBEFP from source you need the following:
 
 - C compiler (with C99 standard and OpenMP support)
@@ -65,8 +69,6 @@ Finally, to install everything issue:
 
     make install
 
-For CMake instructions, see [README-cmake.md](README-cmake.md).
-
 ## Documentation
 
 For a detailed documentation, tutorials, and EFP bibliography check out 
@@ -85,7 +87,7 @@ Fortran bindings to LIBEFP are available in
 The EFPMD program is a molecular simulation package based on LIBEFP.
 It supports EFP-only molecular simulations such as geometry optimization
 and molecular dynamics. EFPMD is a part of the LIBEFP distribution.
-See [this](efpmd/README.md) file for more information.
+See [EFPMD manual](https://libefp2.github.io/efpmd.html) for more information.
 
 ## Parallel scaling
 
@@ -142,36 +144,4 @@ More information can be found in [How to create EFP parameters](https://libefp2.
 
 ## References
 
-1. Fragmentation Methods: A Route to Accurate Calculations on Large Systems.
-   M.S.Gordon, D.G.Fedorov, S.R.Pruitt, L.V.Slipchenko. Chem. Rev. 112, 632-672
-   (2012).
-
-2. Effective fragment method for modeling intermolecular hydrogen bonding
-   effects on quantum mechanical calculations. J.H.Jensen, P.N.Day, M.S.Gordon,
-   H.Basch, D.Cohen, D.R.Garmer, M.Krauss, W.J.Stevens in "Modeling the
-   Hydrogen Bond" (D.A. Smith, ed.) ACS Symposium Series 569, 1994, pp
-   139-151.
-
-3. An effective fragment method for modeling solvent effects in quantum
-   mechanical calculations. P.N.Day, J.H.Jensen, M.S.Gordon, S.P.Webb,
-   W.J.Stevens, M.Krauss, D.Garmer, H.Basch, D.Cohen. J.Chem.Phys. 105,
-   1968-1986 (1996).
-
-4. Solvation of the Menshutkin Reaction: A Rigorous test of the Effective
-   Fragment Model. S.P.Webb, M.S.Gordon. J.Phys.Chem.A 103, 1265-73 (1999).
-
-5. The Effective Fragment Potential Method: a QM-based MM approach to modeling
-   environmental effects in chemistry. M.S.Gordon, M.A.Freitag,
-   P.Bandyopadhyay, J.H.Jensen, V.Kairys, W.J.Stevens. J.Phys.Chem.A 105,
-   293-307 (2001).
-
-6. The Effective Fragment Potential: a general method for predicting
-   intermolecular interactions. M.S.Gordon, L.V.Slipchenko, H.Li, J.H.Jensen.
-   Annual Reports in Computational Chemistry, Volume 3, pp 177-193 (2007).
-
-7. Water-benzene interactions: An effective fragment potential and correlated
-   quantum chemistry study. L.V.Slipchenko, M.S.Gordon. J.Phys.Chem.A 113,
-   2092-2102 (2009).
-
-8. Damping functions in the effective fragment potential method. L.V.Slipchenko,
-   M.S.Gordon. Mol.Phys. 107, 999-1016 (2009).
+A complete list of references to the EFP method can be found [here](https://libefp2.github.io/papers.html#).

compile.sh

@@ -0,0 +1,23 @@
+#!/bin/csh
+
+rm -rf build
+mkdir build
+
+if ( "$TORCH_SWITCH" == "ON" ) then
+    echo "Building with Torch integration..."
+    echo "TORCH_DIR = ${TORCH_INSTALLED_DIR}"
+    cd build
+    setenv TORCH_CXX_FLAGS "-D_GLIBCXX_USE_CXX11_ABI=0"
+    cmake -DCMAKE_INSTALL_PREFIX=${INSTALLATION_DIR} -DCMAKE_PREFIX_PATH=${TORCH_INSTALLED_DIR} -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON ..
+    #cmake -DCMAKE_PREFIX_PATH=${TORCH_INSTALLED_DIR} -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON ..
+    make VERBOSE=1 
+    make install
+else
+    echo "Building without Torch integration..."
+    cmake -H. -Bbuild -DCMAKE_INSTALL_PREFIX=${INSTALLATION_DIR}
+    cd build
+    make VERBOSE=1
+    make install
+endif
+
+echo "Compilation complete. You can now run test jobs as '${INSTALLATION_DIR}/bin/efpmd input.in' from the tests directory."