Merge pull request #6 from d-SEAMS/noGSL

ENH: No GSL

Author: HaoZeke

README.md

@@ -21,7 +21,7 @@
 the data-sets (trajectories) <a
 href="https://figshare.com/projects/d-SEAMS_Datasets/73545">from figshare</a>.
 
-\warning **If** you are unwilling to use the `nix` build system, then **please note** that you must manage the dependencies MANUALLY, including the compiler versions.
+\warning **If** you are unwilling to use the `nix` build system, then **please note** that you must manage the dependencies MANUALLY, including the compiler versions. Optionally, use the provided `conda` environment.
 
 # Citation
 
@@ -49,15 +49,44 @@ The corresponding `bibtex` entry is:
     url={https://doi.org/10.1021/acs.jcim.0c00031}
     }
 
-# Compilation with Nix
+# Compilation
 
 We use a deterministic build system to generate both bug reports and uniform
 usage statistics. This also handles the `lua` scripting engine.
 
 \note The lua functions are documented on the [on the API Docs](https://docs.dseams.info/md_markdown_luafunctions)
 
+We also provide a `conda` environment as a fallback, which is also recommended for MacOS users.
+
 ## Build
 
+### Conda
+
+Although we strongly suggest using `nix`, for MacOS systems, the following
+instructions may be more suitable. We will assume the presence of [micromamba](https://mamba.readthedocs.io/en/latest/installation.html):
+
+```bash
+micromamba create -f environment.yml
+micromamba activate dseams
+```
+
+Now the installation can proceed.
+
+\note we do not install a new version of `cmake` within the `conda` environment because of conflicts with `lua`
+
+```bash
+mkdir build
+cd build
+cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_EXPORT_COMPILE_COMMANDS=YES -DCMAKE_INSTALL_PREFIX:PATH=$CONDA_PREFIX ../
+make -j$(nproc)
+make install
+```
+
+We have opted to install into the `conda` environment, if this is not the
+intended behavior, use `/usr/local` instead.
+
+### Nix
+
 Since this project is built with `nix`, we can simply do the following from the
 root directory (longer method):
 
@@ -87,6 +116,14 @@ nix-env -if . # Required
 yodaStruct -c lua_inputs/config.yml
 ```
 
+### Usage
+
+Having installed the `yodaStruct` binary and library, we can now use it.
+
+```bash
+yodaStruct -c lua_inputs/config.yml
+```
+
 \note The paths in the `.yml` should be **relative to the folder from which the binary is called**.
 
 If you're confused about how to handle the relative paths, run the command `yodaStruct -c lua_inputs/config.yml` in the top-level directory, and set the paths relative to the top-level directory. This is the convention used in the examples as well.

environment.yml

@@ -0,0 +1,22 @@
+# To use:
+#
+#   $ micromamba create -f environment.yml
+#   $ micromamba activate dseams
+#
+name: dseams
+channels:
+  - conda-forge
+dependencies:
+  - compilers
+  - gfortran
+  - catch2
+  - fmt
+  - yaml-cpp
+  - liblapack
+  - libblas
+  - boost-cpp
+  - cmake
+  - lua-luafilesystem
+  # Pinned
+  - eigen==3.3.9
+  - lua==5.2.*

nix/yodaStruct.nix

@@ -21,7 +21,6 @@
 , blas
 , lib
 , boost
-, gsl
 , cmake }:
   clangStdenv.mkDerivation {
   name = "yodaStruct";
@@ -38,7 +37,6 @@
   eigen
   catch2
   boost
-  gsl
   liblapack
   blas
   lua

src/CMakeLists.txt

@@ -17,7 +17,6 @@ set(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR})
 include(FindBLAS)
 include(FindLAPACK)
 include(FindBoost)
-include(FindGSL)
 add_compile_options(
   # "-Wall" "-Wpedantic" "-Wextra" "-fexceptions"
   "$<$<CONFIG:Debug>:-O0;-g3;-ggdb>"
@@ -34,12 +33,10 @@ include_directories(
   ${LUA_INCLUDE_DIR}
   ${Boost_INCLUDE_DIRS}
   ${Eigen3_INCLUDE_DIRS}
-  ${GSL_INCLUDE_DIRS}
   )
 add_definitions(-DBOOST_ERROR_CODE_HEADER_ONLY)
 find_package(
   "Lua" REQUIRED
-  "GSL" REQUIRED
   "Boost" REQUIRED COMPONENTS system filesystem
   "Eigen3 3.3" REQUIRED
   "yaml-cpp"
@@ -52,8 +49,6 @@ target_link_libraries(
   ${Boost_LIBRARIES}
   ${Eigen3_LIBRARIES}
   ${LUA_LIBRARIES}
-  ${GSL_LIBRARIES}
-  stdc++fs
   fmt
   yaml-cpp
   yodaLib

src/bond.cpp

@@ -292,12 +292,12 @@ bond::populateHbonds(std::string filename,
         } // end of applying PBCs to the O-H and O--O vectors
         //
         // Get the angle between the O--O and O-H vectors
-        double gslAngle = gen::gslVecAngle(ooVec, ohVec);
-        double gslAngleDeg = gen::radDeg(gslAngle);
+        double eigenAngle = gen::eigenVecAngle(ooVec, ohVec);
+        double eigenAngleDeg = gen::radDeg(eigenAngle);
 
         //
         // A hydrogen bond is formed if the angle is less than 30 degrees
-        if (gslAngleDeg > angleCutoff) {
+        if (eigenAngleDeg > angleCutoff) {
           continue;
         } // not a hydrogen bond
 

src/generic.cpp

@@ -140,27 +140,18 @@ int gen::unwrappedCoordShift(
 
 /**
  * @details Function for obtaining the angle between two input vectors
- * (std::vector). Internally, the vectors are converted to GSL vectors. The dot
- * product between the input vectors is used to calculate the angle between
+ * (std::vector). Internally, the vectors are converted to Eigen vectors. The
+ * dot product between the input vectors is used to calculate the angle between
  * them.
  * @param[in] OO The O--O vector (but can be any vector, in general).
  * @param[in] OH The O-H vector (but can be any vector, in general).
  * @return The output angle between the input vectors, in radians
  */
-double gen::gslVecAngle(std::vector<double> OO, std::vector<double> OH) {
-  gsl_vector *gOO = gsl_vector_alloc(3);
-  gsl_vector *gOH = gsl_vector_alloc(3);
-  double norm_gOO, norm_gOH, xDummy, angle;
-  for (int i = 0; i < 3; i++) {
-    gsl_vector_set(gOO, i, OO[i]);
-    gsl_vector_set(gOH, i, OH[i]);
-  }
-  norm_gOO = gsl_blas_dnrm2(gOO);
-  norm_gOH = gsl_blas_dnrm2(gOH);
-  gsl_blas_ddot(gOO, gOH, &xDummy);
-  angle = acos(xDummy / (norm_gOO * norm_gOH));
-  gsl_vector_free(gOO);
-  gsl_vector_free(gOH);
+double gen::eigenVecAngle(std::vector<double> OO, std::vector<double> OH) {
+  Eigen::Vector3d eigOO = Eigen::Map<Eigen::Vector3d>(OO.data(), OO.size());
+  Eigen::Vector3d eigOH = Eigen::Map<Eigen::Vector3d>(OH.data(), OH.size());
+  double angle;
+  angle = acos(eigOO.dot(eigOH) / (eigOO.norm() * eigOH.norm()));
   return angle;
 }
 

src/include/internal/generic.hpp

@@ -18,7 +18,9 @@
 
 // Boost
 #include <boost/math/constants/constants.hpp>
-#include <gsl/gsl_blas.h>
+// Eigen
+#include <eigen3/Eigen/Core>
+#include <eigen3/Eigen/Dense>
 
 /** @file generic.hpp
  *   @brief File for containing generic or common functions.
@@ -54,8 +56,8 @@ const double pi = boost::math::constants::pi<double>();
  */
 inline double radDeg(double angle) { return (angle * 180) / gen::pi; }
 
-//! GSL for getting the angle (in radians) between the O--O and O-H vectors
-double gslVecAngle(std::vector<double> OO, std::vector<double> OH);
+//! Eigen function for getting the angle (in radians) between the O--O and O-H vectors
+double eigenVecAngle(std::vector<double> OO, std::vector<double> OH);
 
 //! Get the average, after excluding the outliers, using quartiles
 double getAverageWithoutOutliers(std::vector<double> inpVec);

src/include/internal/mol_sys.hpp

@@ -20,6 +20,7 @@
 #include <string>
 #include <sys/stat.h>
 #include <vector>
+#include<unordered_map>
 
 // For debugging, instantiate the unordered map [consider removal for
 // production]

tests/CMakeLists.txt

@@ -31,15 +31,13 @@ add_executable(yodaStruct_test
 # include(FindBLAS)
 # include(FindLAPACK)
 # include(FindBoost)
-include(FindGSL)
 
 # Find packages
 find_package(
   "Lua" REQUIRED
   "Boost" REQUIRED
   "Eigen3 3.3" REQUIRED
   "Catch2" REQUIRED
-  "GSL" REQUIRED
   "yaml-cpp"
   "fmt"
   )
@@ -49,7 +47,6 @@ target_link_libraries(yodaStruct_test
   ${Boost_LIBRARIES}
   ${Eigen3_LIBRARIES}
   ${LUA_LIBRARIES}
-  ${GSL_LIBRARIES}
   fmt
   yaml-cpp
   yodaLib
@@ -60,7 +57,6 @@ target_link_libraries(yodaStruct_test
 include_directories(
   ${PROJECT_SOURCE_DIR}/src/include/internal
   ${PROJECT_SOURCE_DIR}/src/include/external
-  ${GSL_INCLUDE_DIRS}
   ${Eigen3_INCLUDE_DIRS}
   )
 # Run unit tests