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Add comparison for free energy: Jarzynski eq. vs. thermodynamic integ…
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| Original file line number | Diff line number | Diff line change |
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| # Set the output directory explicitly | ||
| set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/results) | ||
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| # Add the executable for the test | ||
| add_executable(free_energy free_energy.cpp) | ||
| target_link_libraries(free_energy PRIVATE MMFF_lib) |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,116 @@ | ||
| #include "globals.h" | ||
| #include "testUtils.h" | ||
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| #include "MolWorld_sp3.h" | ||
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| char dir_cpp[1024]; | ||
| void init(MolWorld_sp3& W, const char* xyz_name, const char* constr_name=nullptr){ | ||
| W.smile_name = nullptr; | ||
| W.xyz_name = xyz_name; | ||
| W.surf_name = nullptr; | ||
| W.constr_name= constr_name; | ||
| W.bMMFF = true; | ||
| W.bEpairs = false; | ||
| W.gridStep = 0.01; | ||
| W.nPBC = Vec3i({1,1,1}); | ||
| W.bUFF = false; | ||
| W.b141 = true; | ||
| W.bSimple = false; | ||
| W.bConj = true; | ||
| W.bCumulene = true; | ||
| W.bGridFF = false; | ||
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| char path_ElementTypes[1024]; | ||
| char path_AtomTypes[1024]; | ||
| char path_BondTypes[1024]; | ||
| char path_AngleTypes[1024]; | ||
| char path_DihedralTypes[1024]; | ||
| snprintf(path_ElementTypes, sizeof(path_ElementTypes), "%s/common_resources/ElementTypes.dat", dir_cpp); | ||
| snprintf(path_AtomTypes, sizeof(path_AtomTypes), "%s/common_resources/AtomTypes.dat", dir_cpp); | ||
| snprintf(path_BondTypes, sizeof(path_BondTypes), "%s/common_resources/BondTypes.dat", dir_cpp); | ||
| snprintf(path_AngleTypes, sizeof(path_AngleTypes), "%s/common_resources/AngleTypes.dat", dir_cpp); | ||
| snprintf(path_DihedralTypes, sizeof(path_DihedralTypes), "%s/common_resources/DihedralTypes.dat", dir_cpp); | ||
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| verbosity = -1; | ||
| W.initParams( path_ElementTypes, path_AtomTypes, path_BondTypes, path_AngleTypes, path_DihedralTypes); | ||
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| W.init(); | ||
| } | ||
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| void mexican_hat(double lamda1, double lamda2, int nbStep, int nMDsteps, int nEQsteps, double tdamp, double T, double dt, int nbProdSteps, int nrealization, int nSampleSteps){ | ||
| char xyz_path [1024]; | ||
| snprintf(xyz_path, sizeof(xyz_path), "%s/common_resources/xyz/H2O", dir_cpp); | ||
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| MolWorld_sp3 W; | ||
| init(W, xyz_path); | ||
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| // run mexican hat with TI | ||
| W.mexican_hat_TI(lamda1, lamda2, nbStep, nMDsteps, nEQsteps, tdamp, T, dt); | ||
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| // run mexican hat with JE | ||
| W.mexican_hat_JE(lamda1, lamda2, nbProdSteps, nrealization, nEQsteps, tdamp, T, dt, nSampleSteps); | ||
| } | ||
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| void three_atoms_problem(double lamda1, double lamda2, int nbStep, int nMDsteps, int nEQsteps, double tdamp, double T, double dt, int nbProdSteps, int nrealization, int nSampleSteps){ | ||
| char xyz_path [1024]; | ||
| snprintf(xyz_path, sizeof(xyz_path), "%s/common_resources/xyz/H2O", dir_cpp); | ||
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| MolWorld_sp3 W; | ||
| init(W, xyz_path); | ||
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| // run three atom problem with TI | ||
| W.three_atoms_problem_TI(lamda1, lamda2, nbStep, nMDsteps, nEQsteps, tdamp, T, dt); | ||
| // run three atom problem with JE | ||
| W.three_atoms_problem_JE(lamda1, lamda2, nbProdSteps, nrealization, nEQsteps, tdamp, T, dt, nSampleSteps); | ||
| } | ||
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| void entropic_spring(double lamda1, double lamda2, int n, int *dc, int nbStep, int nMDsteps, int nEQsteps, double tdamp, double T, double dt, int nbProdSteps, int nrealization, int nSampleSteps, int natoms){ | ||
| if(!dc){ | ||
| dc = new int[n]; | ||
| for(int i=0; i<n; i++){ | ||
| dc[i] = i; | ||
| printf("%d\n", dc[i]); | ||
| } | ||
| } | ||
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| char xyz_path [1024]; | ||
| snprintf(xyz_path, sizeof(xyz_path), "%s/common_resources/entropic_spring_%d", dir_cpp, natoms); | ||
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| char constr_path [1024]; | ||
| snprintf(constr_path, sizeof(constr_path), "%s/common_resources/entropic_spring_%d.cons", dir_cpp, natoms); | ||
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| MolWorld_sp3 W; | ||
| init(W, xyz_path, constr_path); | ||
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| // run entropic spring with TI | ||
| W.entropic_spring_TI(lamda1, lamda2, n, dc, nbStep, nMDsteps, nEQsteps, tdamp, T, dt); | ||
| // run entropic spring with JE | ||
| W.entropic_spring_JE(lamda1, lamda2, n, dc, nbProdSteps, nrealization, nEQsteps, tdamp, T, dt, nSampleSteps); | ||
| } | ||
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| int main(int argc, char **argv) | ||
| { | ||
| printf("generate data for toy models for free energy\n"); | ||
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| char* current_dir = getcwd(NULL, 0); | ||
| char* cpp_pos = strstr(current_dir, "/cpp"); | ||
| if(cpp_pos) {*(cpp_pos+4) = '\0';} | ||
| else { "Error: cannot find /cpp in current directory path -> Cannot run program"; exit(1); } | ||
| snprintf(dir_cpp, sizeof(dir_cpp), "%s", current_dir); | ||
| free(current_dir); | ||
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| //mexican_hat(std::stod(argv[1]), std::stod(argv[2]), std::stoi(argv[3]), std::stoi(argv[4]), std::stoi(argv[5]), std::stod(argv[6]), std::stod(argv[7]), std::stod(argv[8]), std::stoi(argv[9]), std::stoi(argv[10]), std::stoi(argv[11])); | ||
| //three_atoms_problem(std::stod(argv[1]), std::stod(argv[2]), std::stoi(argv[3]), std::stoi(argv[4]), std::stoi(argv[5]), std::stod(argv[6]), std::stod(argv[7]), std::stod(argv[8]), std::stoi(argv[9]), std::stoi(argv[10]), std::stoi(argv[11])); | ||
| entropic_spring(std::stod(argv[1]), std::stod(argv[2]), 1, nullptr, std::stoi(argv[3]), std::stoi(argv[4]), std::stoi(argv[5]), std::stod(argv[6]), std::stod(argv[7]), std::stod(argv[8]), std::stoi(argv[9]), std::stoi(argv[10]), std::stoi(argv[11]), std::stoi(argv[12])); | ||
| return 0; | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| # plot file TI_plot.dat with gnuplot. In the file, there are 3 columns "lamda", "FreeEnergy" and "Reference", which are the x and 2 y values. Add legend from the header of the file. | ||
| # /bin/python3 /home/kocimil1/Documents/testing_space/Free_energy/Three_particle_problem/main.py | ||
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| gnuplot -e " | ||
| set terminal pngcairo size 1920,1080 enhanced font 'Verdana,10'; | ||
| set output 'results/TI_plot.png'; | ||
| set title 'TI plot'; | ||
| set xlabel 'lamda'; | ||
| set ylabel 'Energy [eV]'; | ||
| set format x '%.1f'; | ||
| set mxtics 5; | ||
| set xtics auto; | ||
| set ytics auto; | ||
| plot 'results/TI_plot.dat' using 1:2:3 with yerrorbars title 'Thermodynamic integration', \ | ||
| 'results/TI_plot.dat' using 1:4 with lines title 'Reference'; | ||
| " | ||
| # show the plot | ||
| display results/TI_plot.png | ||
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