Fixed name

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018 Thomas Murgia
+Copyright (c) 2018 Sasha Murgia
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Makefile

@@ -16,7 +16,7 @@ OBJS := $(shell find $(SRC_DIR) -name "*.o")
 NAME := senpai
 
 WARNINGS := -Wall -Wextra -Werror -Wshadow -Wpointer-arith -Wcast-align -Wwrite-strings -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wuninitialized -Wstrict-prototypes
-OPTIONS := -std=c99 -O2 -g -U__STRICT_ANSI__
+OPTIONS := -fopenmp -std=c99 -O2 -g -U__STRICT_ANSI__
 LIBS := -lm
 CFLAGS := -I$(HDR_DIR) $(WARNINGS) $(OPTIONS) $(LIBS) -o $(NAME).bin
 

README.md

@@ -28,7 +28,7 @@ The simulation is rendered in a cubic universe of constant size, enforcing perio
 
 ## Installation
 
-The first step consists of configuring SENPAI for your machine and use case. This is done by editing the constants in `headers.config.h`.
+The first step consists of configuring SENPAI for your machine and use case. This is done by editing the constants in `headers/config.h`.
 
 On UNIX systems, compilation is achieved using the provided makefile. No additional software is required.
 
@@ -72,25 +72,5 @@ This will tell SENPAI to simulate the contents of `examples/DES.mol` at STP for
 
 This will have SENPAI load 1000 water molecules from `examples/water.mol`, arrange them so that the total potential energy is lower than 100 pJ, and finally simulate the system at 300 Kelvin for 1 ns, saving the render in `water_render.xyz`.
 
-## Questions and Answers
-
-Q: Why are you doing this? Go out, the sun's out.
-
-A: The sun can't simulate deep eutectic solvents.
-
------
-
-Q: Who are you?
-
-A: Thomas Murgia, 19y old at the time of writing this. I'm a second year undergraduate student of chemistry at the Université Toulouse 3 in France.
-
-I plan to keep going with projects like those and hopefully get involved in purely academic and fundamental research in chemistry until the end of my days.
-
------
-
-Q: Are you looking for grad programs? Or even internships?
-
-A: Definitely. E-mail me at <[email protected]> (academic email). I'm open to all offers :)
-
 
 # A complete list of functions and structures is available in the wiki, so as to make contributions easier. Documentation on the way.

examples/DES.mol

@@ -1,5 +1,5 @@
 DES
-Murgia Thomas
+Murgia Sasha
 Deep eutectic solvent (2:1 urea/choline chloride)
  38 34 SENPAI
    -5.4339   -0.6085   -0.9059   17  -1.0  0.418  4.40   1   1   Chloride

examples/co2.mol

@@ -1,5 +1,5 @@
 CO2
-Murgia Thomas
+Murgia Sasha
 A single carbon dioxide molecule
  3 2 SENPAI
    -1.1970    0.0000    0.0000 14  -0.326 0.66931 3.03

examples/dihydrogen.mol

@@ -1,5 +1,5 @@
 Dihydrogen
-Murgia Thomas
+Murgia Sasha
 A single dihydrogen molecule
  2 1 SENPAI
   -0.31 0.0 0.0 2 0.0 0.06 4.02

examples/ethane.mol

@@ -1,5 +1,5 @@
 Ethane
-Murgia Thomas
+Murgia Sasha
 A single ethane molecule
   8  7  SENPAI
    -0.7560    0.0000    0.0000 8   0.0  1.704  4.23

examples/water.mol

@@ -1,5 +1,5 @@
 Water
-Murgia Thomas
+Murgia Sasha
 A single water molecule
  3 2 SENPAI
   0.0000    0.0000    0.0000 18   -0.82  0.650  3.166

headers/text.h

@@ -18,8 +18,8 @@
                     "  \\___ \\|  __| | . ` |  ___/ /\\ \\   | |  \n"\
                     "  ____) | |____| |\\  | |  / ____ \\ _| |_ \n"\
                     " |_____/|______|_| \\_|_| /_/    \\_\\_____|  Simplified Evolutive N-body Processing and Analytics for Integration\n\n"\
-					"<< 2018-2019 Thomas MURGIA - SENPAI and its source code are licensed under the terms of the MIT license >>\n" \
-					"<< [email protected] | https://github.com/Garuda1/senpai >> \n"
+					"<< 2018-2019 Sasha MURGIA - SENPAI and its source code are licensed under the terms of the MIT license >>\n" \
+					"<< [email protected] | https://github.com/Garuda1/senpai >> \n"
 
 
 #define TEXT_FAILURE                           "[" COLOUR_RED "FAILURE" COLOUR_RESET "] "
@@ -79,7 +79,7 @@
 #define TEXT_INFO_ATOMS                                     "Atoms..................%ld\n"
 #define TEXT_INFO_TEMPERATURE                               "Temperature............%lf K\n"
 #define TEXT_INFO_PRESSURE                                  "Pressure...............%lf hPa\n"
-#define TEXT_INFO_DENSITY                                   "Density................%lf g.cm-1\n"
+#define TEXT_INFO_DENSITY                                   "Density................%lf g.cm-3\n"
 #define TEXT_INFO_POTENTIAL_ENERGY                          "Total potential energy.%lf pJ\n"
 #define TEXT_INFO_UNIVERSE_SIZE                             "Universe size  ........%lf pm\n"
 #define TEXT_INFO_SIMULATION_TIME                           "Simulation time........%lf ns\n"

sources/force.c

@@ -199,19 +199,19 @@ universe_t *force_angle(vec3d_t *frc, universe_t *universe, const size_t a1, con
       pos_backup = ligand->pos;
 
       if (to_ligand.x > 0.5*(universe->size))
-        ligand->pos.x -= universe->size;
+        ligand->pos_backup.x -= universe->size;
       else if (to_ligand.x <= -0.5*(universe->size))
-        ligand->pos.x += universe->size;
+        ligand->pos_backup.x += universe->size;
 
       if (to_ligand.y > 0.5*(universe->size))
-        ligand->pos.y -= universe->size;
+        ligand->pos_backup.y -= universe->size;
       else if (to_ligand.y <= -0.5*(universe->size))
-        ligand->pos.y += universe->size;
+        ligand->pos_backup.y += universe->size;
 
       if (to_ligand.z > 0.5*(universe->size))
-        ligand->pos.z -= universe->size;
+        ligand->pos_backup.z -= universe->size;
       else if (to_ligand.z <= -0.5*(universe->size))
-        ligand->pos.z += universe->size;
+        ligand->pos_backup.z += universe->size;
       /* PERIODIC BOUNDARY CONDITIONS */
 
       /* Get its magnitude */
@@ -256,7 +256,7 @@ universe_t *force_total(vec3d_t *frc, universe_t *universe, const size_t atom_id
 {
   size_t i;
   vec3d_t to_target;
-  vec3d_t pos_backup;
+  //vec3d_t pos_backup;
   vec3d_t vec_bond;
   vec3d_t vec_electrostatic;
   vec3d_t vec_lennardjones;
@@ -270,26 +270,27 @@ universe_t *force_total(vec3d_t *frc, universe_t *universe, const size_t atom_id
     {
       /* PERIODIC BOUNDARY CONDITIONS */
       /* Backup the atom's coordinates */
-      pos_backup = universe->atom[i].pos;
+      // pos_backup = universe->atom[i].pos;
+      universe->atom[i].pos_backup = universe->atom[i].pos;
 
       /* Get the vector going to the target atom */
       vec3d_sub(&to_target, &(universe->atom[i].pos), &(universe->atom[atom_id].pos));
 
       /* Temporarily undo the PBC enforcement, if needed */
       if (to_target.x > 0.5*(universe->size))
-        universe->atom[i].pos.x -= universe->size;
+        universe->atom[i].pos_backup.x -= universe->size;
       else if (to_target.x <= -0.5*(universe->size))
-        universe->atom[i].pos.x += universe->size;
+        universe->atom[i].pos_backup.x += universe->size;
 
       if (to_target.y > 0.5*(universe->size))
-        universe->atom[i].pos.y -= universe->size;
+        universe->atom[i].pos_backup.y -= universe->size;
       else if (to_target.y <= -0.5*(universe->size))
-        universe->atom[i].pos.y += universe->size;
+        universe->atom[i].pos_backup.y += universe->size;
 
       if (to_target.z > 0.5*(universe->size))
-        universe->atom[i].pos.z -= universe->size;
+        universe->atom[i].pos_backup.z -= universe->size;
       else if (to_target.z <= -0.5*(universe->size))
-        universe->atom[i].pos.z += universe->size;
+        universe->atom[i].pos_backup.z += universe->size;
       /* PERIODIC BOUNDARY CONDITIONS */
 
       /* Bonded interractions */
@@ -300,7 +301,7 @@ universe_t *force_total(vec3d_t *frc, universe_t *universe, const size_t atom_id
           return (retstr(NULL, TEXT_FORCE_TOTAL_FAILURE, __FILE__, __LINE__));
         if (force_angle(&vec_angle, universe, atom_id, i) == NULL)
           return (retstr(NULL, TEXT_FORCE_TOTAL_FAILURE, __FILE__, __LINE__));
-
+        ;
         /* Sum the forces */
         vec3d_add(frc, frc, &vec_bond);
         vec3d_add(frc, frc, &vec_angle);
@@ -314,13 +315,13 @@ universe_t *force_total(vec3d_t *frc, universe_t *universe, const size_t atom_id
           return (retstr(NULL, TEXT_FORCE_TOTAL_FAILURE, __FILE__, __LINE__));
         if (force_lennardjones(&vec_lennardjones, universe, atom_id, i) == NULL)
           return (retstr(NULL, TEXT_FORCE_TOTAL_FAILURE, __FILE__, __LINE__));
-
+        ;
         /* Sum the forces */
         vec3d_add(frc, frc, &vec_electrostatic);
         vec3d_add(frc, frc, &vec_lennardjones);
       }
       /* Restore the backup coordinates */
-      universe->atom[i].pos = pos_backup;
+      //universe->atom[i].pos = pos_backup;
     }
   }
 

sources/potential.c

@@ -250,25 +250,25 @@ universe_t *potential_total(double *pot, universe_t *universe, const size_t atom
       /* PERIODIC BOUNDARY CONDITIONS */
       /* Backup the atom's coordinates */
       pos_backup = universe->atom[i].pos;
-
+      universe->atom[i].pos_backup = universe->atom[i].pos;
       /* Get the vector going to the target atom */
       vec3d_sub(&to_target, &(universe->atom[i].pos), &(universe->atom[atom_id].pos));
 
       /* Temporarily undo the PBC enforcement, if needed */
       if (to_target.x > 0.5*(universe->size))
-        universe->atom[i].pos.x -= universe->size;
+        universe->atom[i].pos_backup.x -= universe->size;
       else if (to_target.x <= -0.5*(universe->size))
-        universe->atom[i].pos.x += universe->size;
+        universe->atom[i].pos_backup.x += universe->size;
 
       if (to_target.y > 0.5*(universe->size))
-        universe->atom[i].pos.y -= universe->size;
+        universe->atom[i].pos_backup.y -= universe->size;
       else if (to_target.y <= -0.5*(universe->size))
-        universe->atom[i].pos.y += universe->size;
+        universe->atom[i].pos_backup.y += universe->size;
 
       if (to_target.z > 0.5*(universe->size))
-        universe->atom[i].pos.z -= universe->size;
+        universe->atom[i].pos_backup.z -= universe->size;
       else if (to_target.z <= -0.5*(universe->size))
-        universe->atom[i].pos.z += universe->size;
+        universe->atom[i].pos_backup.z += universe->size;
       /* PERIODIC BOUNDARY CONDITIONS */
 
       /* Bonded interractions */
@@ -298,7 +298,7 @@ universe_t *potential_total(double *pot, universe_t *universe, const size_t atom
       }
 
       /* Restore the backup coordinates */
-      universe->atom[i].pos = pos_backup;
+      universe->atom[i].pos_backup = pos_backup;
     }
   }
 

sources/universe.c

@@ -376,43 +376,47 @@ universe_t *universe_iterate(universe_t *universe, const args_t *args)
 {
   size_t i; /* Iterator */
 
+{
   /* We update the position vector first, as part of the Velocity-Verley integration */
   for (i=0; i<(universe->atom_nb); ++i)
     if (atom_update_pos(universe, args, i) == NULL)
-      return (retstr(NULL, TEXT_UNIVERSE_ITERATE_FAILURE, __FILE__, __LINE__));
+      {;} //return (retstr(NULL, TEXT_UNIVERSE_ITERATE_FAILURE, __FILE__, __LINE__));
 
   /* We enforce the periodic boundary conditions */
+
   for (i=0; i<(universe->atom_nb); ++i)
     if (atom_enforce_pbc(universe, i) == NULL)
-      return (retstr(NULL, TEXT_UNIVERSE_ITERATE_FAILURE, __FILE__, __LINE__));
+      {;} //return (retstr(NULL, TEXT_UNIVERSE_ITERATE_FAILURE, __FILE__, __LINE__));
 
   /* Update the force vectors */
   /* By numerically differentiating the potential energy... */
   if (args->numerical == MODE_NUMERICAL)
   {
+    #pragma omp parallel for num_threads(NUM_THREADS)
     for (i=0; i<(universe->atom_nb); ++i)
       if (atom_update_frc_numerical(universe, i) == NULL)
-        return (retstr(NULL, TEXT_UNIVERSE_ITERATE_FAILURE, __FILE__, __LINE__));
+        {;} //return (retstr(NULL, TEXT_UNIVERSE_ITERATE_FAILURE, __FILE__, __LINE__));
   }
 
   /* Or analytically solving for force */
   else
   {
+    #pragma omp parallel for num_threads(NUM_THREADS)
     for (i=0; i<(universe->atom_nb); ++i)
       if (atom_update_frc_analytical(universe, i) == NULL)
-        return (retstr(NULL, TEXT_UNIVERSE_ITERATE_FAILURE, __FILE__, __LINE__));
+        {;} //return (retstr(NULL, TEXT_UNIVERSE_ITERATE_FAILURE, __FILE__, __LINE__));
   }
 
   /* Update the acceleration vectors */
   for (i=0; i<(universe->atom_nb); ++i)
     if (atom_update_acc(universe, i) == NULL)
-      return (retstr(NULL, TEXT_UNIVERSE_ITERATE_FAILURE, __FILE__, __LINE__));
+      {;} //return (retstr(NULL, TEXT_UNIVERSE_ITERATE_FAILURE, __FILE__, __LINE__));
 
   /* Update the speed vectors */
   for (i=0; i<(universe->atom_nb); ++i)
     if (atom_update_vel(universe, args, i) == NULL)
-      return (retstr(NULL, TEXT_UNIVERSE_ITERATE_FAILURE, __FILE__, __LINE__));
-
+      {;} //return (retstr(NULL, TEXT_UNIVERSE_ITERATE_FAILURE, __FILE__, __LINE__));
+}
   return (universe);
 }
 
@@ -652,6 +656,7 @@ universe_t *universe_parameters_print(universe_t *universe, const args_t *args)
 
   /* Print some useful information */
   puts(TEXT_INFO_REFERENCE);
+  printf(TEXT_INFO_THREADS, NUM_THREADS);
   printf(TEXT_INFO_PATH, args->path);
   printf(TEXT_INFO_NAME, universe->meta_name);
   printf(TEXT_INFO_AUTHOR, universe->meta_author);
@@ -673,4 +678,4 @@ universe_t *universe_parameters_print(universe_t *universe, const args_t *args)
   printf(TEXT_INFO_ITERATIONS, (long)ceil(args->max_time/args->timestep));
 
   return (universe);
-}
+}