Merge remote-tracking branch 'origin/master' into pylibefp2

Author: slipchenko

.DS_Store

@@ -143,14 +143,13 @@ jobs:
           activate-environment: libefp-dev
           environment-file: export.yaml
           python-version: ${{ matrix.cfg.python-version }}
-          miniforge-variant: Mambaforge
-          use-mamba: true
-          channels: conda-forge,nodefaults
+          channels: conda-forge
+          conda-remove-defaults: true
 
       - name: Environment Information
         run: |
-          mamba info
-          mamba list
+          conda info
+          conda list
 
       - name: Configure CMake
         run: |
@@ -225,7 +224,7 @@ jobs:
       # Step is unnecessary; remove for debugging.
       - name: Confound Environment - test fetched pybind11
         if: ${{ matrix.cfg.blas == 'OBL' }}
-        run: mamba remove pybind11
+        run: conda remove pybind11
 
       - name: Build & Install Python bindings
         run: |

.github/workflows/ci.yml

@@ -28,4 +28,4 @@ build*/
 /cmake-build-debug/
 comp*.log
 /lib
-
+.DS_Store

.gitignore

@@ -34,6 +34,7 @@ project(
 
 set(CMAKE_INSTALL_PREFIX "$ENV{LIBEFP_DIR}" CACHE PATH "Installation directory" FORCE)
 #set(CMAKE_INSTALL_PREFIX "${LIBEFP_DIR}" CACHE PATH "Installation directory")
+#set(CMAKE_INSTALL_LIBDIR "lib")
 
 ### LVS needs this on MacOS silicon
 set(CMAKE_CXX_STANDARD 17)
@@ -231,6 +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})

CMakeLists.txt

@@ -84,8 +84,10 @@ if(torch_switch)
   message("TORCH_INCLUDE_DIRS =  ${TORCH_INCLUDE_DIRS}")
 endif()
 
+#CXX_STANDARD 14
+
 set_target_properties(efpmd PROPERTIES
-  CXX_STANDARD 14
+  CXX_STANDARD 17
   CXX_STANDARD_REQUIRED YES
 )
 

efpmd/CMakeLists.txt

@@ -147,6 +147,7 @@ static struct cfg *make_cfg(void)
 	cfg_add_bool(cfg, "hess_central", false);
 	cfg_add_double(cfg, "num_step_dist", 0.001);
 	cfg_add_double(cfg, "num_step_angle", 0.01);
+	cfg_add_double(cfg, "pol_damp_value", 0.6);
 
 	cfg_add_enum(cfg, "ensemble", ENSEMBLE_TYPE_NVE,
 		"nve\n"
@@ -351,6 +352,7 @@ static struct efp *create_efp(const struct cfg *cfg, const struct sys *sys)
 		.elec_damp = cfg_get_enum(cfg, "elec_damp"),
 		.disp_damp = cfg_get_enum(cfg, "disp_damp"),
 		.pol_damp = cfg_get_enum(cfg, "pol_damp"),
+		.pol_damp_tt_value = cfg_get_double(cfg, "pol_damp_value"),
 		.pol_driver = cfg_get_enum(cfg, "pol_driver"),
 		.enable_pbc = cfg_get_bool(cfg, "enable_pbc"),
 		.enable_elpot = cfg_get_bool(cfg, "enable_elpot"),
@@ -367,7 +369,7 @@ static struct efp *create_efp(const struct cfg *cfg, const struct sys *sys)
         .print = cfg_get_int(cfg, "print")
 	};
 
-    // adjustoing special terms
+    // adjusting special terms
     if (opts.special_terms == 0) opts.special_terms = opts.terms;
 
 	enum efp_coord_type coord_type = cfg_get_enum(cfg, "coord");
@@ -376,14 +378,6 @@ static struct efp *create_efp(const struct cfg *cfg, const struct sys *sys)
 	if (!efp)
 		error("unable to create efp object");
 
-	if (cfg_get_bool(cfg, "single_params_file"))
-		check_fail(efp_add_potential(efp, cfg_get_string(cfg, "efp_params_file")));
-	else
-		add_potentials(efp, cfg, sys);
-
-	for (size_t i = 0; i < sys->n_frags; i++)
-	    check_fail(efp_add_fragment(efp, sys->frags[i].name));
-
 	if (sys->n_charges > 0) {
 		double q[sys->n_charges];
 		double pos[3 * sys->n_charges];
@@ -407,10 +401,19 @@ static struct efp *create_efp(const struct cfg *cfg, const struct sys *sys)
 	if (cfg_get_bool(cfg, "enable_ff"))
 		opts.terms &= ~(EFP_TERM_ELEC | EFP_TERM_POL | EFP_TERM_DISP | EFP_TERM_XR);
 
+    check_fail(efp_set_opts(efp, &opts));
+
+	if (cfg_get_bool(cfg, "single_params_file"))
+		check_fail(efp_add_potential(efp, cfg_get_string(cfg, "efp_params_file")));
+	else
+		add_potentials(efp, cfg, sys);
+
+	for (size_t i = 0; i < sys->n_frags; i++)
+	    check_fail(efp_add_fragment(efp, sys->frags[i].name));
+
     if (opts.enable_pairwise)
         check_fail(efp_add_ligand(efp, opts.ligand));
 
-    check_fail(efp_set_opts(efp, &opts));
 	check_fail(efp_prepare(efp));
     check_fail(efp_set_symmlist(efp));
 

efpmd/src/main.c

@@ -17,7 +17,7 @@ target_include_directories(ctorch PRIVATE ${TORCH_INCLUDE_DIRS})
 target_link_libraries(ctorch PUBLIC "${TORCH_LIBRARIES}")
 
 set_target_properties(ctorch PROPERTIES
-  CXX_STANDARD 14
+  CXX_STANDARD 17
   CXX_STANDARD_REQUIRED YES
 )