Merge pull request #75 from khavernathy/clean-and-docs

Clean and docs
khavernathy · Apr 21, 2021 · 97f16e8 · 97f16e8
2 parents c209050 + 59b9abb
commit 97f16e8
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Showing 36 changed files with 8,695 additions and 8,055 deletions.
diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
@@ -36,7 +36,7 @@ jobs:
       working-directory: ${{github.workspace}}/build
       shell: bash
       # Execute the build.  You can specify a specific target with "--target <NAME>"
-      run: cmake --build . --config $BUILD_TYPE
+      run: cmake .; make -j1;
 
     - name: Test
       working-directory: ${{github.workspace}}/build

diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,7 @@
+.idea
+Testing
+build
+CTestTestfile.cmake
 *.obj
 *.i
 #md_test

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -14,18 +14,14 @@ configure_file (
 )
 
 set(CMAKE_BUILD_TYPE Release)
-
 set(CMAKE_CXX_FLAGS "-lm -I. -Ofast -foptimize-sibling-calls -finline-limit=10000 -fexpensive-optimizations -flto -frename-registers")
-
 set(CMAKE_CXX_STANDARD 11)
-
 set(INCLUDE src/)
 
 set(SRC 
 src/main.cpp
 )
 
-
 if(MPI)
     message("-- MPI Enabled")
     find_package(MPI REQUIRED)
@@ -38,7 +34,6 @@ else()
     message("-- MPI Disabled")
 endif()
 
-
 if(OMP)
     message("-- OpenMP Enabled")
     find_package(OPENMP REQUIRED)
@@ -57,14 +52,14 @@ else()
     message("-- CUDA Disabled")
 endif()
 
-
-
-
-# make executable
-
 if(CUDA)
     cuda_add_executable(${PROJECT_NAME} ${SRC})
 else()
     add_executable(${PROJECT_NAME} ${SRC})
 endif()
 
+enable_testing()
+add_test(NAME optimize_RuBpy
+        CONFIGURATIONS Release
+        WORKING_DIRECTORY ../examples/optimization/RuBpy
+        COMMAND mcmd mcmd.inp)
diff --git a/src/averages.cpp b/src/averages.cpp
diff --git a/src/boltzmann.cpp b/src/boltzmann.cpp
@@ -25,25 +25,25 @@ double get_boltzmann_factor(System &system, double e_i, double e_f, int_fast8_t
             //fugacity *= 3; // big, but not too big, for biased insertions
             system.constants.bias_uptake_switcher=0; // done biasing if we exceed the bias-N
             printf("Loading bias deactivated! (Desired N reached).\n");
-        }       
+        }
     }
 
     if (system.constants.ensemble == ENSEMBLE_UVT) {
         if (movetype == MOVETYPE_INSERT) {
-            bf = system.pbc.volume * fugacity * 
-            system.constants.ATM2REDUCED/(system.constants.temp * 
-            (double)(system.stats.count_movables)) *
-                exp(-energy_delta/system.constants.temp) *
-                (double)system.proto.size(); // bias for multisorbate (thus no change for single)
+            bf = system.pbc.volume * fugacity *
+                 system.constants.ATM2REDUCED/(system.constants.temp *
+                                               (double)(system.stats.count_movables)) *
+                 exp(-energy_delta/system.constants.temp) *
+                 (double)system.proto.size(); // bias for multisorbate (thus no change for single)
             if (bf < MAXVALUE) system.stats.insert_bf_sum += bf;
             else system.stats.insert_bf_sum += MAXVALUE;
-        } 
+        }
         else if (movetype == MOVETYPE_REMOVE) {
-            bf = system.constants.temp * 
-            ((double)(system.stats.count_movables) + 1.0)/
-            (system.pbc.volume* fugacity *system.constants.ATM2REDUCED) *
-                exp(-energy_delta/system.constants.temp) /
-                (double)system.proto.size(); // bias for multisorbate (thus no change for single)
+            bf = system.constants.temp *
+                 ((double)(system.stats.count_movables) + 1.0)/
+                 (system.pbc.volume* fugacity *system.constants.ATM2REDUCED) *
+                 exp(-energy_delta/system.constants.temp) /
+                 (double)system.proto.size(); // bias for multisorbate (thus no change for single)
             if (bf < MAXVALUE) system.stats.remove_bf_sum += bf;
             else system.stats.remove_bf_sum += MAXVALUE;
         }
@@ -64,11 +64,11 @@ double get_boltzmann_factor(System &system, double e_i, double e_f, int_fast8_t
         if (movetype == MOVETYPE_VOLUME) {
             // Frenkel Smit p118
             bf= exp(-( (energy_delta)
-            + system.constants.pres * system.constants.ATM2REDUCED * 
-            (system.pbc.volume - system.pbc.old_volume)
-            - (system.stats.count_movables + 1) * system.constants.temp * 
-                log(system.pbc.volume/system.pbc.old_volume))/system.constants.temp);
-            
+                       + system.constants.pres * system.constants.ATM2REDUCED *
+                       (system.pbc.volume - system.pbc.old_volume)
+                       - (system.stats.count_movables + 1) * system.constants.temp *
+                       log(system.pbc.volume/system.pbc.old_volume))/system.constants.temp);
+
             if (bf < MAXVALUE) system.stats.volume_change_bf_sum += bf;
             else system.stats.volume_change_bf_sum += MAXVALUE;
         }
@@ -82,17 +82,17 @@ double get_boltzmann_factor(System &system, double e_i, double e_f, int_fast8_t
         if (movetype == MOVETYPE_DISPLACE) {
             double exponent = 3.0*system.stats.count_movables/2.0;
             bf = pow(
-            (system.constants.total_energy - e_f) , exponent) / 
-                pow(
-                    (system.constants.total_energy - e_i) , exponent);
+                     (system.constants.total_energy - e_f), exponent) /
+                 pow(
+                     (system.constants.total_energy - e_i), exponent);
             if (bf < MAXVALUE) system.stats.displace_bf_sum += bf;
             else system.stats.displace_bf_sum += MAXVALUE;
         }
     }
- 
+
     if (bf > MAXVALUE) {
         bf = MAXVALUE;
-    } 
+    }
     else if (std::isinf(bf)) {
         printf("GOT INF! bf = %f\n", bf);
     }