Add std::string save_directory() to set preferred file save path at compile time in IO.hpp

Fixed CMakeLists.txt previously using MPI_C_LIBRARIES to link against MPI_CXX_LIBRARIES

Add optional arguments to build.sh

Add eos.sh to prepare default environment for compiling on Eos

CMakeLists.txt

@@ -6,7 +6,7 @@ find_package(OpenMP REQUIRED)
 find_package(Boost REQUIRED)
 find_package(MPI REQUIRED)
 
-include_directories(${MPI_INCLUDE_PATH})
+include_directories(SYSTEM ${MPI_CXX_INCLUDE_PATH})
 include_directories(./lib/)
 include_directories(./lib/Eigen/)
 include_directories(./lib/GoogleTest/googletest/include/gtest/)
@@ -19,6 +19,7 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
 add_subdirectory(./lib/)
 
 include_directories(./src/)
+include_directories(./src/IO/include/)
 include_directories(./src/Geometry/include/)
 include_directories(./src/Sketch/include/)
 include_directories(./src/Mesh/include/)

apps/CMakeLists.txt

 project(Oersted_Apps)
 
 set(OERSTED_LIBRARIES
+        io
         geometry
         sketch
         elements
@@ -11,7 +12,7 @@ set(OERSTED_LIBRARIES
         physics
         model_templates
         stdc++fs
-        ${MPI_C_LIBRARIES}
+        ${MPI_CXX_LIBRARIES}
         )
 
 add_subdirectory(./Switched\ Winding\ Synchrel)
\ No newline at end of file

apps/Switched Winding Synchrel/main.cpp

 #include "designspace.h"
 #include "globalobjective.h"
 #include "model.h"
+#include "IO.hpp"
 
-#define SUB_DIR "./output/"
+#define SAVE_DIR save_directory() + "/Oersted/output/"
 
 int main(int argc, char** argv) {
     MPI_Init(NULL,NULL);
@@ -26,10 +27,10 @@ int main(int argc, char** argv) {
 
     std::function<ObjectiveMap(Particle)> go = global_objective();
 
-    Swarm swarm{ds,go,swarm_size,objective_tolerance,maximum_iterations,std::greater<double_t>(),global_objective_keys()};
+    Swarm swarm{ds,go,swarm_size,objective_tolerance,maximum_iterations,global_objective_keys(),std::greater<double_t>()};
 
     if (rank == 0) {
-        swarm.set_output_file(SUB_DIR,"sws");
+        swarm.set_output_file(SAVE_DIR,"sws");
     }
 
     double_t dw{1.0/(N-1.0)};

build.sh

 #!/usr/bin/env bash
 
-# TODO: use variable to read in default save directory
+#default arguments
+CMAKE=cmake
+SAVEDIR=$HOME
+
+#parse command line arguments
+while getopts ":c:d:" opt; do
+    case "$opt" in
+        c) CMAKE=$OPTARG;;
+        d) SAVEDIR=$OPTARG;;
+    esac
+done
 
 mkdir -p build
 cd build
 
-export CXX="${CXX:mpic++}"
+export CXXFLAGS="$CXXFLAGS -DSAVEDIR=$SAVEDIR"
 
-export CXXFLAGS="$CXXFLAGS -DSAVEDIR=$MEMBERWORK/phy119"
-
-cmake ..
+$CMAKE ..
 
 make
 

eos.sh

+#!/usr/bin/env bash
+
+module unload PrgEnv-intel PrgEnv-gnu PrgEnv-pgi PrgEnv-cray
+module load PrgEnv-gnu
+module swap gcc gcc/7.2.0
+module load cmake3
\ No newline at end of file

src/CMakeLists.txt

+include_directories(./IO/)
 include_directories(./Geometry/)
 include_directories(./Sketch/)
 include_directories(./Mesh/)
@@ -9,6 +10,7 @@ include_directories(./Optimization/)
 include_directories(./Physics/)
 include_directories(./Model\ Templates/)
 
+add_subdirectory(./IO/)
 add_subdirectory(./Geometry/)
 add_subdirectory(./Sketch/)
 add_subdirectory(./Mesh/)

src/Elements/CMakeLists.txt

@@ -7,7 +7,8 @@ set(SOURCE_FILES
         ./src/Node.cpp      ./src/Node.h
         ./src/Point.cpp     ./src/Point.h
         ./src/Element.cpp   ./src/Element.h
-        ./src/Facet.cpp     ./src/Facet.h)
+        ./src/Facet.cpp     ./src/Facet.h
+        )
 
 add_library(elements STATIC ${SOURCE_FILES})
 

src/IO/CMakeLists.txt

+PROJECT(Oersted_IO)
+
+set(SOURCE_FILES
+        ./include/IO.hpp
+
+        ./src/SaveDirectory.h ./src/SaveDirectory.cpp)
+
+add_library(io STATIC ${SOURCE_FILES})
+
+target_link_libraries(io)
\ No newline at end of file

src/IO/include/IO.hpp

+#ifndef OERSTED_IO_HPP
+#define OERSTED_IO_HPP
+
+#include "../src/SaveDirectory.h"
+
+#endif //OERSTED_IO_HPP

src/IO/src/SaveDirectory.cpp

+#include "SaveDirectory.h"
+
+std::string save_directory() {
+#ifndef SAVEDIR
+    return std::string(std::getenv("HOME"));
+#else
+#define STRINGIFY(x) #x
+#define TO_STRING(x) STRINGIFY(x)
+    return std::string(TO_STRING(SAVEDIR));
+#endif
+}
\ No newline at end of file

src/IO/src/SaveDirectory.h

+#ifndef OERSTED_SAVEDIRECTORY_H
+#define OERSTED_SAVEDIRECTORY_H
+
+#include <string>
+#include <cstdlib>
+
+std::string save_directory();
+
+#endif //OERSTED_SAVEDIRECTORY_H

src/Mesh/src/Mesh.cpp

@@ -937,11 +937,6 @@ void Mesh::save_as(std::string path, std::string file_name) const {
     /*
         This is a stub for visualization
     */
-
-
-    std::string home(std::getenv("HOME"));
-    path = home + path;
-
     if (!std::experimental::filesystem::exists(path)) {
         std::experimental::filesystem::create_directories(path);
     }

src/Optimization/src/Swarm.cpp

@@ -46,9 +46,6 @@ void Swarm::run() {
 }
 
 void Swarm::set_output_file(std::string path, std::string file_name) {
-    std::string home(std::getenv("HOME"));
-    path = home + path;
-
     if (!std::experimental::filesystem::exists(path)) {
         std::experimental::filesystem::create_directories(path);
     }

src/Optimization/src/Swarm.h

@@ -8,7 +8,7 @@
 
 class Swarm {
 public:
-    Swarm(CoordinateSpace ss, std::function<ObjectiveMap(Particle)> go, size_t Np, double_t otol, size_t maxit, std::function<bool(double_t,double_t)> comp = std::less<double_t>(), std::vector<std::string> go_keys = {}) : Space{ss}, GlobalObjective{go}, ObjectiveTolerance{otol}, MaximumIterations{maxit}, Comparator{comp} {
+    Swarm(CoordinateSpace ss, std::function<ObjectiveMap(Particle)> go, size_t Np, double_t otol, size_t maxit, std::vector<std::string> go_keys, std::function<bool(double_t,double_t)> comp = std::less<double_t>()) : Space{ss}, GlobalObjective{go}, ObjectiveTolerance{otol}, MaximumIterations{maxit}, Comparator{comp} {
         std::random_device rd;
         RNG = std::mt19937{rd()};
 

src/Physics/src/FiniteElementMesh.cpp

@@ -272,9 +272,6 @@ std::vector<std::shared_ptr<DiscreteBoundary>> FiniteElementMesh<P, Q>::make_dis
 
 template<size_t P, size_t Q>
 void FiniteElementMesh<P, Q>::write_scalar(Oe::VectorXd const &v, std::string path, std::string file_name) const {
-    std::string home(std::getenv("HOME"));
-    path = home + path;
-
     if (!std::experimental::filesystem::exists(path)) {
         std::experimental::filesystem::create_directories(path);
     }
@@ -318,9 +315,6 @@ void FiniteElementMesh<P, Q>::write_scalar(Oe::VectorXd const &v, std::string pa
 
 template<size_t P, size_t Q>
 void FiniteElementMesh<P, Q>::write_vector(Oe::ArrayXd const &Fx, Oe::ArrayXd const &Fy, std::string path, std::string file_name) const {
-    std::string home(std::getenv("HOME"));
-    path = home + path;
-
     if (!std::experimental::filesystem::exists(path)) {
         std::experimental::filesystem::create_directories(path);
     }

src/Sketch/src/Sketch.cpp

@@ -189,9 +189,6 @@ void Sketch::save_as<SaveMethod::Rasterize>(std::string path, std::string file_n
         This is a stub for visualization
     */
 
-    std::string home(std::getenv("HOME"));
-    path = home + path;
-
     if (!std::experimental::filesystem::exists(path)) {
         std::experimental::filesystem::create_directories(path);
     }

test/CMakeLists.txt

@@ -59,6 +59,7 @@ set(MPI_SOURCE_FILES
 set(LINK_LIBRARIES
         gtest
         gtest_main
+        io
         geometry
         sketch
         elements
@@ -69,7 +70,7 @@ set(LINK_LIBRARIES
         physics
         model_templates
         stdc++fs
-        ${MPI_C_LIBRARIES}
+        ${MPI_CXX_LIBRARIES}
         )
 
 add_executable(run_tests ${SOURCE_FILES})

test/LibraryIntegration/Library_Integration_Test.hpp

@@ -3,6 +3,7 @@
 
 #include "gtest.h"
 
+#include "IO.hpp"
 #include "Sketch.hpp"
 #include "Mesh.hpp"
 #include "Quadrature.hpp"

test/LibraryIntegration/Mesh_To_FEM_Test.cpp

 #include "Library_Integration_Test.hpp"
 
-#define SUB_DIR std::string("/Oersted/test/output/Integration/")
+#define SAVE_DIR save_directory()+"/Oersted/test/output/Integration/"
 
 TEST(Full_Circle, Magnetostatic_Uniform_Current_Density) {
     // Create Sketch
@@ -28,7 +28,7 @@ TEST(Full_Circle, Magnetostatic_Uniform_Current_Density) {
 
     EXPECT_EQ(sk.size_contours(), 1);
 
-    sk.save_as<SaveMethod::Rasterize>(SUB_DIR, std::string("full_circle_sketch"));
+    sk.save_as<SaveMethod::Rasterize>(SAVE_DIR, std::string("full_circle_sketch"));
 
     // Create Refineable Mesh
     Mesh me{sk};
@@ -40,7 +40,7 @@ TEST(Full_Circle, Magnetostatic_Uniform_Current_Density) {
 
     me.refine();
 
-    me.save_as(SUB_DIR, std::string("full_circle_mesh"));
+    me.save_as(SAVE_DIR, std::string("full_circle_mesh"));
 
     // Convert to FiniteElementMesh
     auto fem = std::make_shared<FiniteElementMesh<1,1>>(me);
@@ -102,7 +102,7 @@ TEST(Full_Circle, Magnetostatic_Uniform_Current_Density) {
 
     // Save
     Eigen::VectorXd vv = msph.recover_boundary(solution->v);
-    fem->write_scalar(vv, SUB_DIR, std::string("full_circle_magnetostatic_uniform_current_density"));
+    fem->write_scalar(vv, SAVE_DIR, std::string("full_circle_magnetostatic_uniform_current_density"));
 
     // Test
     msph.linearize(solution);
@@ -180,7 +180,7 @@ public:
         bool result = sk.build();
         ASSERT_TRUE(result);
 
-        sk.save_as<SaveMethod::Rasterize>(SUB_DIR, "sixth_circle_mirror_copy_sketch");
+        sk.save_as<SaveMethod::Rasterize>(SAVE_DIR, "sixth_circle_mirror_copy_sketch");
 
         periodic_boundary = sk.select_periodic_boundary_pairs(v0, 60.0);
         {
@@ -255,7 +255,7 @@ public:
         bool result = me.refine();
         ASSERT_TRUE(result);
 
-        me.save_as(SUB_DIR, std::string("sixth_circle_mirror_copy_mesh"));
+        me.save_as(SAVE_DIR, std::string("sixth_circle_mirror_copy_mesh"));
 
         // Create FiniteElementMesh
         fem = std::make_shared<FiniteElementMesh<1, 1>>(me);
@@ -361,7 +361,7 @@ TEST_F(Sixth_Circle_Mirror_Copy, Magnetostatic_Uniform_Current_Density_Periodic)
     // A = a_f * r^2 + c_f in forced inner region
     // A = a_h * log(r) + c_h in homogeneous outer region
     Eigen::VectorXd vv = msph.recover_boundary(solution->v);
-    fem->write_scalar(vv, SUB_DIR, std::string("sixth_circle_uniform_current_density_periodic"));
+    fem->write_scalar(vv, SAVE_DIR, std::string("sixth_circle_uniform_current_density_periodic"));
 
     double_t a_f = -0.5;
     double_t c_f = -2.0 * a_f * std::log(2.0) - a_f;
@@ -455,7 +455,7 @@ TEST_F(Sixth_Circle_Mirror_Copy, Magnetostatic_Uniform_Current_Density_Antieriod
     // Bounds are obtained from the Fourier series approximation of the square wave current density
 
     Eigen::VectorXd vv = msph.recover_boundary(solution->v);
-    fem->write_scalar(vv, SUB_DIR, std::string("sixth_circle_uniform_current_density_antiperiodic"));
+    fem->write_scalar(vv, SAVE_DIR, std::string("sixth_circle_uniform_current_density_antiperiodic"));
 
     double_t a_f = -2.0 / (5.0);
     double_t b_f = -384.0 / 321.0 * a_f;
@@ -522,7 +522,7 @@ public:
         bool result = sk.build();
         ASSERT_TRUE(result);
 
-        sk.save_as<SaveMethod::Rasterize>(SUB_DIR, "sixth_circle_sketch");
+        sk.save_as<SaveMethod::Rasterize>(SAVE_DIR, "sixth_circle_sketch");
 
         periodic_boundary = sk.select_periodic_boundary_pairs(v0, 60.0);
         {
@@ -597,7 +597,7 @@ public:
         bool result = me.refine();
         ASSERT_TRUE(result);
 
-        me.save_as(SUB_DIR, std::string("sixth_circle_mesh"));
+        me.save_as(SAVE_DIR, std::string("sixth_circle_mesh"));
 
         // Create FiniteElementMesh
         fem = std::make_shared<FiniteElementMesh<1, 1>>(me);
@@ -724,7 +724,7 @@ TEST_F(Sixth_Circle, Magnetostatic_Uniform_Current_Density_Periodic_Rotation) {
         // A = a_f * r^2 + c_f in forced inner region
         // A = a_h * log(r) + c_h in homogeneous outer region
         Eigen::VectorXd vv = msph.recover_boundary(solution->v);
-        fem->write_scalar(vv, SUB_DIR, std::string("one_sixth_circle_uniform_current_density_periodic_rotation_") + std::to_string(iter));
+        fem->write_scalar(vv, SAVE_DIR, std::string("one_sixth_circle_uniform_current_density_periodic_rotation_") + std::to_string(iter));
 
         double_t a_f = -0.5;
         double_t c_f = -2.0 * a_f * std::log(2.0) - a_f;
@@ -826,7 +826,7 @@ TEST_F(Sixth_Circle, Magnetostatic_Uniform_Current_Density_Antiperiodic_Rotation
         // Bounds are obtained from the Fourier series approximation of the square wave current density
 
         Eigen::VectorXd vv = msph.recover_boundary(solution->v);
-        fem->write_scalar(vv, SUB_DIR, std::string("sixth_circle_uniform_current_density_antiperiodic_") + std::to_string(iter));
+        fem->write_scalar(vv, SAVE_DIR, std::string("sixth_circle_uniform_current_density_antiperiodic_") + std::to_string(iter));
 
         double_t a_f = -2.0 / (5.0);
         double_t b_f = -384.0 / 321.0 * a_f;
@@ -997,7 +997,7 @@ public:
         residual = sk.solve();
         EXPECT_LE(residual, FLT_EPSILON * rro);
 
-        sk.save_as<SaveMethod::Rasterize>(SUB_DIR, std::string("salient_pole_synchrel_sketch"));
+        sk.save_as<SaveMethod::Rasterize>(SAVE_DIR, std::string("salient_pole_synchrel_sketch"));
 
         bool result = sk.build();
         EXPECT_TRUE(result);
@@ -1024,7 +1024,7 @@ public:
         EXPECT_TRUE(me.edges_are_valid());
         EXPECT_TRUE(me.edges_are_optimal());
 
-        me.save_as(SUB_DIR, std::string("salient_pole_synchrel_mesh"));
+        me.save_as(SAVE_DIR, std::string("salient_pole_synchrel_mesh"));
 
         //me.MaximumElementSize = 5.0e-3;
         me.MinimumElementQuality = 0.5;
@@ -1032,7 +1032,7 @@ public:
         // Refine and save
         me.refine();
 
-        me.save_as(SUB_DIR, std::string("salient_pole_synchrel_mesh"));
+        me.save_as(SAVE_DIR, std::string("salient_pole_synchrel_mesh"));
 
         // Create FiniteElementMesh
         fem = std::make_shared<FiniteElementMesh<2, 2>>(me); // TODO: Look at speeding this up somehow, try row major sparse matrix operators, sparse vectors for evaluation of magnetization
@@ -1176,11 +1176,11 @@ TEST_F(Salient_Pole_Synchrel, Test) {
 
         // Save image
         Eigen::VectorXd vv = msph->recover_boundary(solution->v);
-        fem->write_scalar(vv, SUB_DIR, std::string("salient_pole_syncrel_A_") + std::to_string(iter));
+        fem->write_scalar(vv, SAVE_DIR, std::string("salient_pole_syncrel_A_") + std::to_string(iter));
 
         Eigen::ArrayXd Bx = msph->derivatives().dy(0).transpose() * solution->v;
         Eigen::ArrayXd By = -msph->derivatives().dx(0).transpose() * solution->v;
-        fem->write_vector(Bx, By, SUB_DIR, std::string("salient_pole_synchrel_B_") + std::to_string(iter));
+        fem->write_vector(Bx, By, SAVE_DIR, std::string("salient_pole_synchrel_B_") + std::to_string(iter));
 
         // Increment Position
         *position += step;

test/LibraryIntegration/test_Annuli.cpp

@@ -36,7 +36,7 @@ public:
         bool result = sk.build();
         ASSERT_TRUE(result);
 
-        sk.save_as<SaveMethod::Rasterize>(SUB_DIR, std::string("sketch"));
+        sk.save_as<SaveMethod::Rasterize>(SAVE_DIR, std::string("sketch"));
 
         BoundingBall bi = BoundingBall{0.0,0.0,1.0+FLT_EPSILON};
         BoundingBall bo = BoundingBall{0.0,0.0,2.0+FLT_EPSILON};
@@ -64,10 +64,10 @@ public:
         bool result = me.refine();
         ASSERT_TRUE(result);
 
-        me.save_as(SUB_DIR, std::string("mesh"));
+        me.save_as(SAVE_DIR, std::string("mesh"));
     }
 
-    std::string SUB_DIR = "/Oersted/output/Integration/test_Annuli/";
+    std::string SAVE_DIR = save_directory()+"/Oersted/output/Integration/test_Annuli/";
 
     std::vector<std::shared_ptr<Curve>> inner_boundaries;
     std::vector<std::shared_ptr<Curve>> outer_boundaries;