d_atoms.c

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/* This file is part of the 'atomes' software
 
'atomes' is free software: you can redistribute it and/or modify it under the terms
of the GNU Affero General Public License as published by the Free Software Foundation,
either version 3 of the License, or (at your option) any later version.
 
'atomes' is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
 
You should have received a copy of the GNU Affero General Public License along with 'atomes'.
If not, see <https://www.gnu.org/licenses/>
 
Copyright (C) 2022-2025 by CNRS and University of Strasbourg */
 
/*
* This file: 'd_atoms.c'
*
* Contains:
*
 
 - The functions to prepare the OpenGL rendering atom(s) and clone(s)
 
*
* List of functions:
 
  int sphere_vertices (int qual);
  int sphere_indices (int qual);
  int find_atom_vertices (gboolean to_pick);
  int find_clone_vertices (gboolean to_pick);
 
  float get_sphere_radius (int style, int sp, int ac, int sel);
 
  void setup_sphere_vertice (float * vertices, vec3_t pos, ColRGBA col, float rad, float alpha);
  void setup_this_atom (int style, gboolean to_pick, gboolean picked, atom * at, int ac, float * vert, float al);
  void setup_atom_vertices (int style, gboolean to_pick, float * vertices);
  void prepare_clone (int style, gboolean to_pick, int picked, atom at, atom bt, float x, float y, float z, float * vertices);
  void setup_clone_vertices (int style, gboolean to_pick, float * vertices);
  void atom_positions_colors_and_sizes (int style, gboolean to_pick, float * instances);
  void create_atom_lists (gboolean to_pick);
 
  ColRGBA get_atom_color (int i, int j, double al, int picked, gboolean to_pick);
 
  object_3d * draw_sphere (int quality);
 
*/
 
#include "global.h"
#include "glview.h"
#include "ogl_shading.h"
#include "dlp_field.h"
#include "preferences.h"
 
int atom_id;
int gColorID[3];
int all_styles[NUM_STYLES];
 
ColRGBA get_atom_color (int i, int j, double al, int picked, gboolean to_pick)
{
  // i = atom spec, j = atom id (for coordination maps), al = alpha
  int s = i;
  int m;
  ColRGBA colo;
  if (to_pick)
  {
    gColorID[0]++;
    if(gColorID[0] > 255)
    {
      gColorID[0] = 0;
      gColorID[1]++;
      if(gColorID[1] > 255)
      {
        gColorID[1] = 0;
        gColorID[2]++;
      }
    }
    wingl -> color_to_pick[wingl -> to_be_picked] = gColorID[0] + 256*gColorID[1] + 256*256*gColorID[2];
    colo.red = gColorID[0]/255.0;
    colo.green = gColorID[1]/255.0;
    colo.blue = gColorID[2]/255.0;
    colo.alpha = 1.0;
    wingl -> to_be_picked ++;
  }
  else if (picked)
  {
    if (field_color)
    {
      colo = init_color (proj_gl -> atoms[step][j].coord[4], num_field_objects);
      colo.alpha = DEFAULT_OPACITY*0.75;
    }
    else
    {
      colo = plot -> sel_color[(picked == 1) ? 0 : 1];
    }
  }
  else
  {
    if (acolorm == 0)
    {
      colo.red = plot -> at_color[s].red;
      colo.green = plot -> at_color[s].green;
      colo.blue = plot -> at_color[s].blue;
      colo.alpha = al;// * plot -> m_terial.param[5];
    }
    else if (acolorm < 5)
    {
      if (acolorm < 3)
      {
        s -= proj_sp*(s/proj_sp);
      }
      else
      {
        s = 0;
      }
      int k = proj_gl -> atoms[step][j].coord[acolorm -1];
      colo.red = plot -> spcolor[acolorm - 1][s][k].red;
      colo.green = plot -> spcolor[acolorm - 1][s][k].green;
      colo.blue = plot -> spcolor[acolorm - 1][s][k].blue;
      colo.alpha = al;// * plot -> m_terial.param[5];
    }
    else if (acolorm == 5)
    {
      field_molecule * fmol = get_active_field_molecule_from_model_id (proj_gl, j);
      if (fmol)
      {
        s = proj_gl -> atoms[0][j].fid;
        m = fmol -> mol -> natoms;
      }
      else
      {
        s = 0;
        m = 1;
      }
      colo = init_color (s, m);
      colo.alpha = al;// * plot -> m_terial.param[5];
    }
    else if (acolorm == 6)
    {
      colo.red = wingl -> custom_map -> colors[step][j].red;
      colo.blue = wingl -> custom_map -> colors[step][j].blue;
      colo.green = wingl -> custom_map -> colors[step][j].green;
      colo.alpha = wingl -> custom_map -> colors[step][j].alpha;
    }
  }
  return colo;
}
 
int nbs, nbl, nba;
 
int sphere_vertices (int qual)
{
  return qual * qual;
}
 
int sphere_indices (int qual)
{
  return 2 * qual * (qual - 1);
}
 
object_3d * draw_sphere (int quality)
{
  float theta, phi;
  float cos_phi, sin_phi;
  float xPos, yPos, zPos;
  int stack, slice;
  int x, y, z;
 
  object_3d * new_sphere = g_malloc0 (sizeof*new_sphere);
  new_sphere -> quality = quality;
  new_sphere -> num_vertices = sphere_vertices (quality);
  new_sphere -> vert_buffer_size = 3;
  new_sphere -> vertices = allocfloat (3*new_sphere -> num_vertices);
  new_sphere -> num_indices = sphere_indices (quality);
  new_sphere -> ind_buffer_size = 1;
  new_sphere -> indices = allocint (new_sphere -> num_indices);
  x = 0;
  for (stack=0; stack <= quality-1; stack++)
  {
    phi = pi * stack / (quality-1);
    cos_phi = cos(phi);
    sin_phi = sin(phi);
    for (slice=0; slice <= quality-1; slice++)
    {
      theta = 2.0 * pi * slice / (quality-1);
      xPos = cos(theta) * sin_phi;
      yPos = cos_phi;
      zPos = sin(theta) * sin_phi;
      new_sphere -> vertices[3*x]   = xPos;
      new_sphere -> vertices[3*x+1] = yPos;
      new_sphere -> vertices[3*x+2] = zPos;
      x ++;
    }
  }
 
  gboolean oddRow = FALSE;
  z = 0;
  for (y = 0; y < quality-1; y++)
  {
    if (!oddRow) // even rows: y == 0, y == 2; and so on
    {
      for (x = 0; x <= quality-1; x++)
      {
        new_sphere -> indices[z] = (y * quality + x);
        new_sphere -> indices[z+1]= ((y + 1) * quality + x);
        z += 2;
      }
    }
    else
    {
      for (x = quality-1; x >= 0; x--)
      {
        new_sphere -> indices[z] = ((y + 1) * quality + x);
        new_sphere -> indices[z+1] = (y * quality + x);
        z += 2;
      }
    }
    oddRow = !oddRow;
  }
  return new_sphere;
}
 
float get_sphere_radius (int style, int sp, int ac, int sel)
{
  if (style == WIREFRAME || style == PUNT)
  {
    return plot -> pointrad[sp + ac*proj_sp] + sel*4.0;
  }
  else if (style == SPACEFILL)
  {
    return plot -> atomicrad[sp + ac*proj_sp] + sel*0.05;
  }
  else if (style == CYLINDERS)
  {
    return plot -> radall[ac] + sel*0.1;
  }
  else
  {
    return plot -> sphererad[sp + ac*proj_sp] + sel*0.05;
  }
}
 
void setup_sphere_vertice (float * vertices, vec3_t pos, ColRGBA col, float rad, float alpha)
{
  int l;
  l = nbl*ATOM_BUFF_SIZE;
  vertices[l]   = pos.x;
  vertices[l+1] = pos.y;
  vertices[l+2] = pos.z;
  vertices[l+3] = rad;
  vertices[l+4] = col.red;
  vertices[l+5] = col.green;
  vertices[l+6] = col.blue;
  vertices[l+7] = col.alpha * alpha;
  nbl ++;
}
 
void setup_this_atom (int style, gboolean to_pick, gboolean picked, atom * at, int ac, float * vert, float al)
{
  int i, j, k;
  float alpha = 1.0;
  float shift[3];
  ColRGBA col = get_atom_color (at -> sp, at -> id, 1.0, picked, to_pick);
  if (at -> sp > proj_sp - 1) at -> sp -= proj_sp;
  float rad = get_sphere_radius ((style == NONE) ? plot -> style : style, at -> sp, ac, (picked) ? 1 : 0);
  for (i=0; i<plot -> abc -> extra_cell[0]+1;i++)
  {
    for (j=0; j<plot -> abc -> extra_cell[1]+1; j++)
    {
      for (k=0; k<plot -> abc -> extra_cell[2]+1; k++)
      {
        shift[0]=i*box_gl -> vect[0][0]+j*box_gl -> vect[1][0]+k*box_gl -> vect[2][0];
        shift[1]=i*box_gl -> vect[0][1]+j*box_gl -> vect[1][1]+k*box_gl -> vect[2][1];
        shift[2]=i*box_gl -> vect[0][2]+j*box_gl -> vect[1][2]+k*box_gl -> vect[2][2];
        at_shift (at, shift);
        setup_sphere_vertice (vert, vec3(at -> x, at -> y, at -> z), col, rad, (to_pick) ? 1.0 : alpha*al);
        at_unshift (at, shift);
        alpha = 0.5;
      }
    }
  }
}
 
int find_atom_vertices (gboolean to_pick)
{
  int i, j;
  j = 0;
  for (i=0; i<proj_at; i++)
  {
    if (in_movie_encoding && plot -> at_data != NULL)
    {
      if (plot -> at_data[i].show[0])
      {
        if (to_pick)
        {
          all_styles[0] ++;
        }
        else
        {
          all_styles[plot -> at_data[i].style + 1] ++;
        }
        j ++;
      }
    }
    else
    {
      if (proj_gl -> atoms[step][i].show[0])
      {
        if (to_pick)
        {
          all_styles[0] ++;
        }
        else
        {
          all_styles[proj_gl -> atoms[step][i].style + 1] ++;
        }
        j ++;
      }
    }
  }
  return j;
}
 
void setup_atom_vertices (int style, gboolean to_pick, float * vertices)
{
  int i;
  atom * tmp_a;
  for (i=0; i<proj_at; i++)
  {
    tmp_a = duplicate_atom (& proj_gl -> atoms[step][i]);
    if (in_movie_encoding && plot -> at_data != NULL)
    {
      tmp_a -> show[0] = plot -> at_data[i].show[0];
      tmp_a -> style = plot -> at_data[i].style;
    }
    if (tmp_a -> show[0] && (tmp_a -> style == style || to_pick))
    {
      setup_this_atom (style, to_pick, 0, tmp_a, 0, vertices, 1.0);
    }
    g_free (tmp_a);
  }
}
 
void prepare_clone (int style, gboolean to_pick, int picked, atom at, atom bt, float x, float y, float z, float * vertices)
{
  atom * tmp_a = duplicate_atom (& bt);
  tmp_a -> x += x;
  tmp_a -> y += y;
  tmp_a -> z += z;
  tmp_a -> id = at.id;
  tmp_a -> sp = at.sp + proj_sp;
  int sty = at.style;
  if (in_movie_encoding && plot -> at_data != NULL)
  {
    tmp_a -> show[1] = plot -> at_data[at.id].show[1];
    sty = plot -> at_data[at.id].style;
  }
  if (at.show[1] && (sty == style || to_pick))
  {
    setup_this_atom (style, to_pick, picked, tmp_a, 1, vertices, 0.5);
  }
  g_free (tmp_a);
}
 
int find_clone_vertices (gboolean to_pick)
{
  int i, j, k, l;
  l = 0;
  for (i=0; i < wingl -> bonds[step][1]; i++)
  {
    j = wingl -> bondid[step][1][i][0];
    k = wingl -> bondid[step][1][i][1];
    if (in_movie_encoding && plot -> at_data != NULL)
    {
      if (plot -> at_data[j].show[1])
      {
        if (to_pick)
        {
          all_styles[0] ++;
        }
        else
        {
          all_styles[plot -> at_data[j].style + 1] ++;
        }
        l++;
      }
      if (plot -> at_data[k].show[1])
      {
        if (to_pick)
        {
          all_styles[0] ++;
        }
        else
        {
          all_styles[plot -> at_data[k].style + 1] ++;
        }
        l++;
      }
    }
    else
    {
      if (proj_gl -> atoms[step][j].show[1])
      {
        if (to_pick)
        {
          all_styles[0] ++;
        }
        else
        {
          all_styles[proj_gl -> atoms[step][j].style + 1] ++;
        }
        l ++;
      }
      if (proj_gl -> atoms[step][k].show[1])
      {
        if (to_pick)
        {
          all_styles[0] ++;
        }
        else
        {
          all_styles[proj_gl -> atoms[step][k].style + 1] ++;
        }
        l ++;
      }
    }
  }
  return l;
}
 
void setup_clone_vertices (int style, gboolean to_pick, float * vertices)
{
  int i, j, k;
  for (i=0; i < wingl -> bonds[step][1]; i++)
  {
    j = wingl -> bondid[step][1][i][0];
    k = wingl -> bondid[step][1][i][1];
    prepare_clone (style, to_pick, 0,
                   proj_gl -> atoms[step][j],
                   proj_gl -> atoms[step][k],
                   wingl -> clones[step][i].x,
                   wingl -> clones[step][i].y,
                   wingl -> clones[step][i].z, vertices);
    prepare_clone (style, to_pick, 0,
                   proj_gl -> atoms[step][k],
                   proj_gl -> atoms[step][j],
                  -wingl -> clones[step][i].x,
                  -wingl -> clones[step][i].y,
                  -wingl -> clones[step][i].z, vertices);
 
  }
}
 
void atom_positions_colors_and_sizes (int style, gboolean to_pick, float * instances)
{
  setup_atom_vertices (style, to_pick, instances);
  if (to_pick) wingl -> atoms_to_be_picked = wingl -> clones_to_be_picked = wingl -> to_be_picked;
  if (plot -> draw_clones)
  {
    setup_clone_vertices (style, to_pick, instances);
    if (to_pick) wingl -> clones_to_be_picked = wingl -> to_be_picked;
  }
}
 
void create_atom_lists (gboolean to_pick)
{
  int i, j, k;
  object_3d * atos;
  gboolean sphere = TRUE;
 
  if (! to_pick)
  {
    cleaning_shaders (wingl, ATOMS);
    wingl -> create_shaders[ATOMS] = FALSE;
  }
 
  for (i=0; i<NUM_STYLES; i++) all_styles[i] = 0;
  j = find_atom_vertices (to_pick);
  if (plot -> draw_clones) j += find_clone_vertices (to_pick);
#ifdef DEBUG
  g_debug ("Atom LIST:: to_pick= %s, Atom(s) to render= %d", (to_pick) ? "true" : "false", j);
#endif
  if (j > 0)
  {
    // Render atom(s)
    j = (plot -> abc -> extra_cell[0]+1)*(plot -> abc -> extra_cell[1]+1)*(plot -> abc -> extra_cell[2]+1);
    if (! to_pick)
    {
      wingl -> n_shaders[ATOMS][step] = 0;
      for (i=0; i<NUM_STYLES; i++) if (all_styles[i]) wingl -> n_shaders[ATOMS][step] ++;
      wingl -> ogl_glsl[ATOMS][step] = g_malloc0 (wingl -> n_shaders[ATOMS][step]*sizeof*wingl -> ogl_glsl[ATOMS][step]);
    }
    k = 0;
    for (i=0; i<NUM_STYLES; i++)
    {
      sphere = TRUE;
      if (all_styles[i] || to_pick)
      {
        if (! i)
        {
          if (plot -> style == WIREFRAME || plot -> style == PUNT) sphere = FALSE;
        }
        else
        {
          if (i-1 == WIREFRAME || i-1 == PUNT) sphere = FALSE;
        }
        if (sphere)
        {
          atos = draw_sphere (plot -> quality);
        }
        else
        {
          atos = g_malloc0 (sizeof*atos);
          atos -> vert_buffer_size = 3;
          atos -> num_vertices = 1;
          atos -> vertices = allocfloat (3);
          atos -> vertices[0] = atos -> vertices[1] = atos -> vertices[2] = 0.0;
        }
        atos -> num_instances = j*all_styles[i];
        atos -> inst_buffer_size = ATOM_BUFF_SIZE;
        atos -> instances = allocfloat (j*all_styles[i]*ATOM_BUFF_SIZE);
        nbl = 0;
        atom_positions_colors_and_sizes (i-1, to_pick, atos -> instances);
        if (! to_pick)
        {
          if (sphere)
          {
            wingl -> ogl_glsl[ATOMS][step][k] = init_shader_program (ATOMS, GLSL_SPHERES, sphere_vertex, NULL, full_color, GL_TRIANGLE_STRIP, 4, 1, TRUE, atos);
          }
          else
          {
            wingl -> ogl_glsl[ATOMS][step][k] = init_shader_program (ATOMS, GLSL_POINTS, point_vertex, NULL, point_color, GL_POINTS, 4, 1, FALSE, atos);
          }
        }
        else
        {
          wingl -> ogl_glsl[PICKS][0][0] = init_shader_program (PICKS, GLSL_SPHERES, sphere_vertex, NULL, full_color, GL_TRIANGLE_STRIP, 4, 1, FALSE, atos);
        }
        g_free (atos);
        k ++;
      }
      if (to_pick) break;
    }
  }
}