__editor_maybe_static int load_board_direct(struct board *cur_board,
FILE *fp, int data_size, int savegame, int version)
{
int num_robots, num_scrolls, num_sensors, num_robots_active;
int overlay_mode, size, board_width, board_height, i;
int viewport_x, viewport_y, viewport_width, viewport_height;
int truncated = 0;
struct robot *cur_robot;
struct scroll *cur_scroll;
struct sensor *cur_sensor;
char *test_buffer;
int board_location = ftell(fp);
cur_board->num_robots = 0;
cur_board->num_robots_allocated = 0;
cur_board->num_robots_active = 0;
cur_board->num_scrolls = 0;
cur_board->num_scrolls_allocated = 0;
cur_board->num_sensors = 0;
cur_board->num_sensors_allocated = 0;
cur_board->robot_list = NULL;
cur_board->robot_list_name_sorted = NULL;
cur_board->sensor_list = NULL;
cur_board->scroll_list = NULL;
// Initialize some fields that may no longer be loaded
// from the board file itself..
cur_board->last_key = '?';
cur_board->num_input = 0;
cur_board->input_size = 0;
cur_board->input_string[0] = 0;
cur_board->player_last_dir = 0x10;
cur_board->bottom_mesg[0] = 0;
cur_board->b_mesg_timer = 0;
cur_board->lazwall_start = 7;
cur_board->b_mesg_row = 24;
cur_board->b_mesg_col = -1;
cur_board->scroll_x = 0;
cur_board->scroll_y = 0;
cur_board->locked_x = -1;
cur_board->locked_y = -1;
cur_board->volume = 255;
cur_board->volume_inc = 0;
cur_board->volume_target = 255;
// board_mode, unused
if(fgetc(fp) == EOF)
{
val_error(WORLD_BOARD_MISSING, board_location);
return VAL_MISSING;
}
overlay_mode = fgetc(fp);
if(!overlay_mode)
{
int overlay_width;
int overlay_height;
overlay_mode = fgetc(fp);
overlay_width = fgetw(fp);
overlay_height = fgetw(fp);
size = overlay_width * overlay_height;
if((size < 1) || (size > MAX_BOARD_SIZE))
goto err_invalid;
cur_board->overlay = cmalloc(size);
cur_board->overlay_color = cmalloc(size);
if(load_RLE2_plane(cur_board->overlay, fp, size))
goto err_freeoverlay;
test_buffer = cmalloc(1024);
free(test_buffer);
// Skip sizes
if(fseek(fp, 4, SEEK_CUR) ||
load_RLE2_plane(cur_board->overlay_color, fp, size))
goto err_freeoverlay;
test_buffer = cmalloc(1024);
free(test_buffer);
}
else
{
overlay_mode = 0;
// Undo that last get
fseek(fp, -1, SEEK_CUR);
}
cur_board->overlay_mode = overlay_mode;
board_width = fgetw(fp);
board_height = fgetw(fp);
cur_board->board_width = board_width;
cur_board->board_height = board_height;
size = board_width * board_height;
if((size < 1) || (size > MAX_BOARD_SIZE))
goto err_freeoverlay;
cur_board->level_id = cmalloc(size);
cur_board->level_color = cmalloc(size);
cur_board->level_param = cmalloc(size);
cur_board->level_under_id = cmalloc(size);
cur_board->level_under_color = cmalloc(size);
cur_board->level_under_param = cmalloc(size);
if(load_RLE2_plane(cur_board->level_id, fp, size))
goto err_freeboard;
if(fseek(fp, 4, SEEK_CUR) ||
load_RLE2_plane(cur_board->level_color, fp, size))
goto err_freeboard;
if(fseek(fp, 4, SEEK_CUR) ||
load_RLE2_plane(cur_board->level_param, fp, size))
goto err_freeboard;
if(fseek(fp, 4, SEEK_CUR) ||
load_RLE2_plane(cur_board->level_under_id, fp, size))
goto err_freeboard;
if(fseek(fp, 4, SEEK_CUR) ||
load_RLE2_plane(cur_board->level_under_color, fp, size))
goto err_freeboard;
if(fseek(fp, 4, SEEK_CUR) ||
load_RLE2_plane(cur_board->level_under_param, fp, size))
goto err_freeboard;
// Load board parameters
if(version < 0x0253)
{
fread(cur_board->mod_playing, LEGACY_MOD_FILENAME_MAX, 1, fp);
cur_board->mod_playing[LEGACY_MOD_FILENAME_MAX] = 0;
}
else
{
size_t len = fgetw(fp);
if(len >= MAX_PATH)
len = MAX_PATH - 1;
fread(cur_board->mod_playing, len, 1, fp);
cur_board->mod_playing[len] = 0;
}
viewport_x = fgetc(fp);
viewport_y = fgetc(fp);
viewport_width = fgetc(fp);
viewport_height = fgetc(fp);
if(
(viewport_x < 0) || (viewport_x > 79) ||
(viewport_y < 0) || (viewport_y > 24) ||
(viewport_width < 1) || (viewport_width > 80) ||
(viewport_height < 1) || (viewport_height > 25))
goto err_invalid;
cur_board->viewport_x = viewport_x;
cur_board->viewport_y = viewport_y;
cur_board->viewport_width = viewport_width;
cur_board->viewport_height = viewport_height;
cur_board->can_shoot = fgetc(fp);
cur_board->can_bomb = fgetc(fp);
cur_board->fire_burn_brown = fgetc(fp);
cur_board->fire_burn_space = fgetc(fp);
cur_board->fire_burn_fakes = fgetc(fp);
cur_board->fire_burn_trees = fgetc(fp);
cur_board->explosions_leave = fgetc(fp);
cur_board->save_mode = fgetc(fp);
cur_board->forest_becomes = fgetc(fp);
cur_board->collect_bombs = fgetc(fp);
cur_board->fire_burns = fgetc(fp);
for(i = 0; i < 4; i++)
{
cur_board->board_dir[i] = fgetc(fp);
}
cur_board->restart_if_zapped = fgetc(fp);
cur_board->time_limit = fgetw(fp);
if(version < 0x0253)
{
cur_board->last_key = fgetc(fp);
cur_board->num_input = fgetw(fp);
cur_board->input_size = fgetc(fp);
fread(cur_board->input_string, LEGACY_INPUT_STRING_MAX + 1, 1, fp);
cur_board->input_string[LEGACY_INPUT_STRING_MAX] = 0;
cur_board->player_last_dir = fgetc(fp);
fread(cur_board->bottom_mesg, LEGACY_BOTTOM_MESG_MAX + 1, 1, fp);
cur_board->bottom_mesg[LEGACY_BOTTOM_MESG_MAX] = 0;
cur_board->b_mesg_timer = fgetc(fp);
cur_board->lazwall_start = fgetc(fp);
cur_board->b_mesg_row = fgetc(fp);
cur_board->b_mesg_col = (signed char)fgetc(fp);
cur_board->scroll_x = (signed short)fgetw(fp);
cur_board->scroll_y = (signed short)fgetw(fp);
cur_board->locked_x = (signed short)fgetw(fp);
cur_board->locked_y = (signed short)fgetw(fp);
}
else if(savegame)
{
size_t len;
cur_board->last_key = fgetc(fp);
cur_board->num_input = fgetw(fp);
cur_board->input_size = fgetw(fp);
len = fgetw(fp);
if(len >= ROBOT_MAX_TR)
len = ROBOT_MAX_TR - 1;
fread(cur_board->input_string, len, 1, fp);
cur_board->input_string[len] = 0;
cur_board->player_last_dir = fgetc(fp);
len = fgetw(fp);
if(len >= ROBOT_MAX_TR)
len = ROBOT_MAX_TR - 1;
fread(cur_board->bottom_mesg, len, 1, fp);
cur_board->bottom_mesg[len] = 0;
cur_board->b_mesg_timer = fgetc(fp);
cur_board->lazwall_start = fgetc(fp);
cur_board->b_mesg_row = fgetc(fp);
cur_board->b_mesg_col = (signed char)fgetc(fp);
cur_board->scroll_x = (signed short)fgetw(fp);
cur_board->scroll_y = (signed short)fgetw(fp);
cur_board->locked_x = (signed short)fgetw(fp);
cur_board->locked_y = (signed short)fgetw(fp);
}
cur_board->player_ns_locked = fgetc(fp);
cur_board->player_ew_locked = fgetc(fp);
cur_board->player_attack_locked = fgetc(fp);
if(version < 0x0253 || savegame)
{
cur_board->volume = fgetc(fp);
cur_board->volume_inc = fgetc(fp);
cur_board->volume_target = fgetc(fp);
}
/***************/
/* Load robots */
/***************/
num_robots = fgetc(fp);
num_robots_active = 0;
if(num_robots == EOF)
truncated = 1;
// EOF/crazy value check
if((num_robots < 0) || (num_robots > 255) || (num_robots > size))
goto board_scan;
cur_board->robot_list = ccalloc(num_robots + 1, sizeof(struct robot *));
// Also allocate for name sorted list
cur_board->robot_list_name_sorted =
ccalloc(num_robots, sizeof(struct robot *));
// Any null objects being placed will later be optimized out
if(num_robots)
{
for(i = 1; i <= num_robots; i++)
{
// Make sure there's robots to load here
int length_check = fgetw(fp);
fseek(fp, -2, SEEK_CUR);
if(length_check < 0)
{
// Send off the error and then tell validation to shut up for now
val_error(WORLD_ROBOT_MISSING, ftell(fp));
set_validation_suppression(1);
truncated = 1;
}
cur_robot = load_robot_allocate(fp, savegame, version);
if(cur_robot->used)
{
cur_board->robot_list[i] = cur_robot;
cur_board->robot_list_name_sorted[num_robots_active] = cur_robot;
num_robots_active++;
}
else
{
// We don't need no null robot
clear_robot(cur_robot);
cur_board->robot_list[i] = NULL;
}
}
}
set_validation_suppression(-1);
if(num_robots_active > 0)
{
if(num_robots_active != num_robots)
{
cur_board->robot_list_name_sorted =
crealloc(cur_board->robot_list_name_sorted,
sizeof(struct robot *) * num_robots_active);
}
qsort(cur_board->robot_list_name_sorted, num_robots_active,
sizeof(struct robot *), cmp_robots);
}
else
{
free(cur_board->robot_list_name_sorted);
cur_board->robot_list_name_sorted = NULL;
}
cur_board->num_robots = num_robots;
cur_board->num_robots_allocated = num_robots;
cur_board->num_robots_active = num_robots_active;
/****************/
/* Load scrolls */
/****************/
num_scrolls = fgetc(fp);
if(num_scrolls == EOF)
truncated = 1;
if((num_scrolls < 0) || (num_scrolls > 255) || (num_robots + num_scrolls > size))
goto board_scan;
cur_board->scroll_list = ccalloc(num_scrolls + 1, sizeof(struct scroll *));
if(num_scrolls)
{
for(i = 1; i <= num_scrolls; i++)
{
cur_scroll = load_scroll_allocate(fp);
if(cur_scroll->used)
cur_board->scroll_list[i] = cur_scroll;
else
clear_scroll(cur_scroll);
}
}
cur_board->num_scrolls = num_scrolls;
cur_board->num_scrolls_allocated = num_scrolls;
/****************/
/* Load sensors */
/****************/
num_sensors = fgetc(fp);
if(num_sensors == EOF)
truncated = 1;
if((num_sensors < 0) || (num_sensors > 255) ||
(num_scrolls + num_sensors + num_robots > size))
goto board_scan;
cur_board->sensor_list = ccalloc(num_sensors + 1, sizeof(struct sensor *));
if(num_sensors)
{
for(i = 1; i <= num_sensors; i++)
{
cur_sensor = load_sensor_allocate(fp);
if(cur_sensor->used)
cur_board->sensor_list[i] = cur_sensor;
else
clear_sensor(cur_sensor);
}
}
cur_board->num_sensors = num_sensors;
cur_board->num_sensors_allocated = num_sensors;
board_scan:
// Now do a board scan to make sure there aren't more than the data told us.
{
int robot_count = 0, scroll_count = 0, sensor_count = 0;
char err_mesg[80] = { 0 };
for(i = 0; i < (board_width * board_height); i++)
{
if(cur_board->level_id[i] > 127)
cur_board->level_id[i] = CUSTOM_BLOCK;
if(cur_board->level_under_id[i] > 127)
cur_board->level_under_id[i] = CUSTOM_FLOOR;
switch(cur_board->level_id[i])
{
case ROBOT:
case ROBOT_PUSHABLE:
{
robot_count++;
if(robot_count > cur_board->num_robots)
{
cur_board->level_id[i] = CUSTOM_BLOCK;
cur_board->level_param[i] = 'R';
cur_board->level_color[i] = 0xCF;
}
break;
}
case SIGN:
case SCROLL:
{
scroll_count++;
if(scroll_count > cur_board->num_scrolls)
{
cur_board->level_id[i] = CUSTOM_BLOCK;
cur_board->level_param[i] = 'S';
cur_board->level_color[i] = 0xCF;
}
}
case SENSOR:
{
// Wait, I forgot. Nobody cares about sensors.
//sensor_count++;
if(sensor_count > cur_board->num_sensors)
{
cur_board->level_id[i] = CUSTOM_FLOOR;
cur_board->level_param[i] = 'S';
cur_board->level_color[i] = 0xDF;
}
}
}
}
if(robot_count > cur_board->num_robots)
{
snprintf(err_mesg, 80, "Board @ %Xh: found %i robots; expected %i",
board_location, robot_count, cur_board->num_robots);
error(err_mesg, 1, 8, 0);
}
if(scroll_count > cur_board->num_scrolls)
{
snprintf(err_mesg, 80, "Board @ %Xh: found %i scrolls/signs; expected %i",
board_location, scroll_count, cur_board->num_scrolls);
error(err_mesg, 1, 8, 0);
}
// This won't be reached but I'll leave it anyway.
if(sensor_count > cur_board->num_sensors)
{
snprintf(err_mesg, 80, "Board @ %Xh: found %i sensors; expected %i",
board_location, sensor_count, cur_board->num_sensors);
error(err_mesg, 1, 8, 0);
}
if(err_mesg[0])
error("Any extra robots/scrolls/signs were replaced", 1, 8, 0);
}
if(truncated == 1)
val_error(WORLD_BOARD_TRUNCATED_SAFE, board_location);
return VAL_SUCCESS;
err_freeboard:
free(cur_board->level_id);
free(cur_board->level_color);
free(cur_board->level_param);
free(cur_board->level_under_id);
free(cur_board->level_under_color);
free(cur_board->level_under_param);
err_freeoverlay:
if(overlay_mode)
{
free(cur_board->overlay);
free(cur_board->overlay_color);
}
err_invalid:
val_error(WORLD_BOARD_CORRUPT, board_location);
return VAL_INVALID;
}
__editor_maybe_static void __set_config_from_file(
find_change_option find_change_handler, void *conf, const char *conf_file_name)
{
char current_char, *input_position, *output_position, *use_extended_buffer;
int line_size, extended_size, extended_allocate_size = 512;
char line_buffer_alternate[256], line_buffer[256];
int extended_buffer_offset, peek_char;
char *extended_buffer;
char *equals_position, *value;
FILE *conf_file;
conf_file = fopen(conf_file_name, "rb");
if(!conf_file)
return;
extended_buffer = cmalloc(extended_allocate_size);
while(fsafegets(line_buffer_alternate, 255, conf_file))
{
if(line_buffer_alternate[0] != '#')
{
input_position = line_buffer_alternate;
output_position = line_buffer;
equals_position = NULL;
do
{
current_char = *input_position;
if(!isspace((int)current_char))
{
if((current_char == '\\') &&
(input_position[1] == 's'))
{
input_position++;
current_char = ' ';
}
if((current_char == '=') && (equals_position == NULL))
equals_position = output_position;
*output_position = current_char;
output_position++;
}
input_position++;
} while(current_char);
if(equals_position)
{
*equals_position = 0;
value = equals_position + 1;
}
else
{
value = (char *)"1";
}
if(line_buffer[0])
{
// There might be extended information too - get it.
peek_char = fgetc(conf_file);
extended_size = 0;
extended_buffer_offset = 0;
use_extended_buffer = NULL;
while((peek_char == ' ') || (peek_char == '\t'))
{
// Extended data line
use_extended_buffer = extended_buffer;
if(fsafegets(line_buffer_alternate, 254, conf_file))
{
line_size = (int)strlen(line_buffer_alternate);
line_buffer_alternate[line_size] = '\n';
line_size++;
extended_size += line_size;
if(extended_size >= extended_allocate_size)
{
extended_allocate_size *= 2;
extended_buffer = crealloc(extended_buffer,
extended_allocate_size);
}
strcpy(extended_buffer + extended_buffer_offset,
line_buffer_alternate);
extended_buffer_offset += line_size;
}
peek_char = fgetc(conf_file);
}
ungetc(peek_char, conf_file);
find_change_handler(conf, line_buffer, value, use_extended_buffer);
}
}
}
free(extended_buffer);
fclose(conf_file);
}
void set_atm_params(DICT_WORD atm_dict[],int num_atm_dict,
char fun_key[],char filename[],
int jmol_typ,int jres, int jres_off,
CPATOM_MAPS *cpatom_maps,MDATOM_MAPS *atommaps,
BUILD_INTRA *build_intra,MDCLATOMS_INFO *clatoms_info,
MDGHOST_ATOMS *ghost_atoms,MDCONSTRNT *mdconstrnt)
/*=======================================================================*/
{/*begin routine*/
/*=======================================================================*/
/* Local Variables */
NAME site;
int i,iii,num,num2,num3,num4,iatm_ind,imask,index,num1;
int itype,iatm_ind_sm,ifound;
double dnum;
/*=======================================================================*/
/* I) Check for missing key words */
for(i=1;i<=num_atm_dict;i++){
if(atm_dict[i].iuset==0 && atm_dict[i].key_type==1){
keyword_miss(atm_dict,filename,fun_key,i);}
}/*endfor*/
/*=======================================================================*/
/* II) Get atm index */
sscanf(atm_dict[2].keyarg,"%d",&iatm_ind);
index = 2;
if(iatm_ind>build_intra->natmind_1res_now||iatm_ind<0){
keyarg_barf(atm_dict,filename,fun_key,index);}
imask = build_intra->mask_atm[iatm_ind];
/*=======================================================================*/
/*=======================================================================*/
if(imask>0){
/*=======================================================================*/
/* III) Get rejiggered atm index */
/*-----------------------------------------------------------------------*/
iatm_ind = (build_intra->index_atm)[iatm_ind];
if(iatm_ind>build_intra->natm_1res_now||iatm_ind<0){
keyarg_barf(atm_dict,filename,fun_key,index);}
build_intra->iatm_ind_chk[iatm_ind]++;
iatm_ind_sm = iatm_ind;
iatm_ind = iatm_ind + clatoms_info->natm_tot;
/*=======================================================================*/
/* IV) Fill the dictionary with words */
/*-----------------------------------------------------------------------*/
/* 3) \mass{} */
sscanf(atm_dict[3].keyarg,"%lg",&dnum);
index = 3;
if(dnum<=0.0){
keyarg_barf(atm_dict,filename,fun_key,index);
}/*endif*/
clatoms_info->mass[iatm_ind] = dnum;
/*--------------------------------------------------------------------*/
/* 4) \charge{} */
sscanf(atm_dict[4].keyarg,"%lg",&dnum);
clatoms_info->q[iatm_ind] = dnum;
/*--------------------------------------------------------------------*/
/* 5) \alpha_pol{} */
sscanf(atm_dict[5].keyarg,"%lg",&dnum);
index = 5;
if(dnum<0.0){
keyarg_barf(atm_dict,filename,fun_key,index);
}/*endif*/
clatoms_info->alp_pol[iatm_ind] = dnum;
/*--------------------------------------------------------------------*/
/* 6) \b_neut{} */
sscanf(atm_dict[6].keyarg,"%lg",&dnum);
clatoms_info->b_neut[iatm_ind] = dnum;
/*--------------------------------------------------------------------*/
/* 7) \valence{} */
sscanf(atm_dict[7].keyarg,"%d",&num);
build_intra->bond_site[iatm_ind_sm].valence = num;
index = 7;
if(num<0||num>MAX_VALENCE){
keyarg_barf(atm_dict,filename,fun_key,index);}
/*--------------------------------------------------------------------*/
/* 8) \improper_def{} */
strcpy(build_intra->strip1,atm_dict[8].keyarg);
parse_improp(build_intra->strip1,build_intra->strip2,&num1,&num2,&num3,
&num4);
build_intra->bond_site[iatm_ind_sm].improper_ind[1]=num1+1;
build_intra->bond_site[iatm_ind_sm].improper_ind[2]=num2+1;
build_intra->bond_site[iatm_ind_sm].improper_ind[3]=num3+1;
build_intra->bond_site[iatm_ind_sm].improper_ind[4]=num4+1;
index = 8;
if((num1+num2+num3+num4)!=0&&(num1+num2+num3+num4)!=6){
keyarg_barf(atm_dict,filename,fun_key,index);}
if((num1+num2+num3+num4)==6){
if(num1<0||num1>3||num2<0||num2>3||num3<0||num3>3||num4<0||num4>3||
num1==num2||num1==num3||num2==num3||num1==num4||num2==num4||
num3==num4){
keyarg_barf(atm_dict,filename,fun_key,index);}}
/*--------------------------------------------------------------------*/
/* 9) \bond_site_1{} */
strcpy(build_intra->strip1,atm_dict[9].keyarg);
parse_bond_site(build_intra->strip1,build_intra->strip2,site,&num2,&num3);
strcpy(build_intra->bond_site[iatm_ind_sm].bond_site_name[1],site);
build_intra->bond_site[iatm_ind_sm].branch_1[1] = num2;
build_intra->bond_site[iatm_ind_sm].branch_2[1] = num3;
index = 9;
if(strlen(site)==0||num2<-1||num3<-1||num2>MAX_VALENCE||num3>MAX_VALENCE){
keyarg_barf(atm_dict,filename,fun_key,index);
}/*endif*/
/*--------------------------------------------------------------------*/
/* 10) \bond_site_2{} */
strcpy(build_intra->strip1,atm_dict[10].keyarg);
parse_bond_site(build_intra->strip1,build_intra->strip2,site,&num2,&num3);
strcpy(build_intra->bond_site[iatm_ind_sm].bond_site_name[2],site);
build_intra->bond_site[iatm_ind_sm].branch_1[2] = num2;
build_intra->bond_site[iatm_ind_sm].branch_2[2] = num3;
index = 10;
if(strlen(site)==0||num2<-1||num3<-1||num2>MAX_VALENCE||num3>MAX_VALENCE){
keyarg_barf(atm_dict,filename,fun_key,index);
}
/*---------------------------------------------------------------------*/
/* 11) \bond_site_3{} */
strcpy(build_intra->strip1,atm_dict[11].keyarg);
parse_bond_site(build_intra->strip1,build_intra->strip2,site,&num2,&num3);
strcpy(build_intra->bond_site[iatm_ind_sm].bond_site_name[3],site);
build_intra->bond_site[iatm_ind_sm].branch_1[3] = num2;
build_intra->bond_site[iatm_ind_sm].branch_2[3] = num3;
index = 11;
if(strlen(site)==0||num2<-1||num3<-1||num2>MAX_VALENCE||num3>MAX_VALENCE){
keyarg_barf(atm_dict,filename,fun_key,index);}
/*---------------------------------------------------------------------*/
/* 12) \bond_site_4{} */
strcpy(build_intra->strip1,atm_dict[12].keyarg);
parse_bond_site(build_intra->strip1,build_intra->strip2,site,&num2,&num3);
strcpy(build_intra->bond_site[iatm_ind_sm].bond_site_name[4],site);
build_intra->bond_site[iatm_ind_sm].branch_1[4] = num2;
build_intra->bond_site[iatm_ind_sm].branch_2[4] = num3;
index = 12;
if(strlen(site)==0||num2<-1||num3<-1||num2>MAX_VALENCE||num3>MAX_VALENCE){
keyarg_barf(atm_dict,filename,fun_key,index);}
/*------------------------------------------------------------------------*/
/* 15) \cp_atom{} */
ifound = 0;
if(strcasecmp(atm_dict[15].keyarg,"yes")==0){
ifound=1;cpatom_maps->cp_atm_flag[iatm_ind] = 1;
}
if(strcasecmp(atm_dict[15].keyarg,"no")==0){
ifound=1;cpatom_maps->cp_atm_flag[iatm_ind] = 0;
}
/*--------------------------------------------------------------------*/
/* 13) \cp_valence_up{} */
cpatom_maps->cp_vlnc_up[iatm_ind] = 0;
if(atm_dict[13].iuset==1){
sscanf(atm_dict[13].keyarg,"%d",&num);
cpatom_maps->cp_vlnc_up[iatm_ind] = num;
}/*endif*/
if(atm_dict[13].iuset==0 && cpatom_maps->cp_atm_flag[iatm_ind]==1){
index = 13;
keyarg_barf(atm_dict,filename,fun_key,index);
}/*endif*/
/*--------------------------------------------------------------------*/
/* 14) \cp_valence_dn{} */
cpatom_maps->cp_vlnc_dn[iatm_ind] = cpatom_maps->cp_vlnc_up[iatm_ind];
if(atm_dict[14].iuset == 1){
sscanf(atm_dict[14].keyarg,"%d",&num);
cpatom_maps->cp_vlnc_dn[iatm_ind] = num;
}/*endif*/
/*------------------------------------------------------------------------*/
/* 16) /def_ghost1{} */
ghost_atoms->ighost_flag[iatm_ind] = 0;
if(atm_dict[16].iuset!=0){
set_ghost(ghost_atoms,clatoms_info,atommaps,build_intra,
atm_dict,num_atm_dict,
filename,fun_key,iatm_ind);
}/*endif*/
/*------------------------------------------------------------------------*/
/* 17) \label{} */
index = 16+NCOEF_GHOST_MAX;
ifound = 0;
if(strcasecmp(atm_dict[index].keyarg,"standard")==0){
ifound=1;mdconstrnt->atom_label[iatm_ind] = 0;
}
if(strcasecmp(atm_dict[index].keyarg,"backbone")==0){
ifound=1;mdconstrnt->atom_label[iatm_ind] = 1;
}
if(strcasecmp(atm_dict[index].keyarg,"sidechain")==0){
ifound=1;mdconstrnt->atom_label[iatm_ind] = 2;
}
if(ifound==0){
keyarg_barf(atm_dict,filename,fun_key,index);
}/*endif*/
/*--------------------------------------------------------------------*/
/* 18+NCOEF_GHOST_MAX) \cp_valence_true_up{} */
cpatom_maps->cp_vlnc_true_up[iatm_ind] = cpatom_maps->cp_vlnc_up[iatm_ind];
if(atm_dict[18+NCOEF_GHOST_MAX].iuset == 1){
sscanf(atm_dict[18+NCOEF_GHOST_MAX].keyarg,"%d",&num);
cpatom_maps->cp_vlnc_true_up[iatm_ind] = num;
if (num>cpatom_maps->cp_vlnc_up[iatm_ind]){
index = 18+NCOEF_GHOST_MAX;
keyarg_barf(atm_dict,filename,fun_key,index);
}/*endif*/
}/*endif*/
/*--------------------------------------------------------------------*/
/* 19+NCOEF_GHOST_MAX) \cp_valence_true_dn{} */
cpatom_maps->cp_vlnc_true_dn[iatm_ind] = cpatom_maps->cp_vlnc_true_up[iatm_ind];
if(atm_dict[19+NCOEF_GHOST_MAX].iuset == 1){
sscanf(atm_dict[19+NCOEF_GHOST_MAX].keyarg,"%d",&num);
cpatom_maps->cp_vlnc_true_dn[iatm_ind] = num;
if (num>cpatom_maps->cp_vlnc_dn[iatm_ind]){
index = 19+NCOEF_GHOST_MAX;
keyarg_barf(atm_dict,filename,fun_key,index);
}/*endif*/
}/*endif*/
/*------------------------------------------------------------------------*/
/*====================================================================*/
/* IV) Do up atom types */
itype = atommaps->natm_typ + 1;
for(i=1;i<=atommaps->natm_typ;i++){
if(strcasecmp(atm_dict[1].keyarg,atommaps->atm_typ[i])==0)
itype=i;
} /*endfor*/
if(itype>build_intra->natm_typ_max){
build_intra->natm_typ_max+=NMEM_MIN;
atommaps->atm_typ = (NAME *)
crealloc(&(atommaps->atm_typ[1]),
(build_intra->natm_typ_max)*sizeof(NAME),"set_atm_params")-1;
}/*endif*/
if(itype==atommaps->natm_typ+1){
atommaps->natm_typ+=1;
strcpy(atommaps->atm_typ[itype],atm_dict[1].keyarg);
}/*endif*/
/*====================================================================*/
/* V) Do up types */
atommaps->iatm_mol_typ[iatm_ind] = jmol_typ;
atommaps->iatm_mol_num[iatm_ind] = 1;
atommaps->iatm_res_num[iatm_ind] = jres;
atommaps->iatm_atm_typ[iatm_ind] = itype;
atommaps->iatm_res_typ[iatm_ind] =
atommaps->ires_typ_jres_jmol_typ[jres+jres_off];
/*====================================================================*/
/*====================================================================*/
} /*endif (imask>0) */
/*======================================================================*/
} /*end routine*/
int cFunctionalsVecToVec::myConfigureInstance()
{
int i,j;
cComponentManager *_compman = getCompMan();
if (_compman != NULL) {
int nTp = _compman->getNtypes();
nFunctTp = 0;
for (i=0; i<nTp; i++) {
const char * tp = _compman->getComponentType(i,1);
if (tp!=NULL) {
if (!strncmp(tp,"cFunctional",11)&&strcmp(tp,COMPONENT_NAME_CFUNCTIONALSVECTOVEC)) {
// find beginning "cFunctional" but not our own type (cFunctinals)
const char *fn = tp+11;
if (nFunctTpAlloc == nFunctTp) { // realloc:
functTp = (char **)crealloc( functTp, sizeof(char*)*(nFunctTpAlloc+N_BLOCK_ALLOC), nFunctTpAlloc );
functTpI = (int *)crealloc( functTpI, sizeof(int)*(nFunctTpAlloc+N_BLOCK_ALLOC), nFunctTpAlloc );
functI = (int *)crealloc( functI, sizeof(int)*(nFunctTpAlloc+N_BLOCK_ALLOC), nFunctTpAlloc );
functN = (int *)crealloc( functN, sizeof(int)*(nFunctTpAlloc+N_BLOCK_ALLOC), nFunctTpAlloc );
functObj = (cFunctionalComponent **)crealloc( functObj, sizeof(cFunctionalComponent *)*(nFunctTpAlloc+N_BLOCK_ALLOC), nFunctTpAlloc );
nFunctTpAlloc += N_BLOCK_ALLOC;
}
functTp[nFunctTp] = strdup(fn);
functTpI[nFunctTp] = i;
nFunctTp++;
}
}
}
}
SMILE_DBG(2,"(inst '%s') found %i cFunctionalXXXX component types.",getInstName(),nFunctTp);
// fetch enabled functionals list
nFunctionalsEnabled = getArraySize("functionalsEnabled");
nFunctValues = 0;
requireSorted = 0;
for (i=0; i<nFunctionalsEnabled; i++) {
const char *fname = getStr_f(myvprint("functionalsEnabled[%i]",i));
char *tpname = myvprint("cFunctional%s",fname);
for (j=0; j<nFunctTp; j++) {
if (!strcmp(functTp[j],fname)) {
functI[i] = j;
break;
}
}
// TODO: find duplicates in functionalsEnabled Array!!!
if (j<nFunctTp) {
// and create corresponding component instances...
SMILE_DBG(3,"(inst '%s') creating Functional object 'cFunctional%s'.",fname);
char *_tmp = myvprint("%s.%s",getInstName(),fname);
cFunctionalComponent * tmp = (cFunctionalComponent *)(_compman->createComponent)(_tmp,tpname);
free(_tmp);
if (tmp==NULL) OUT_OF_MEMORY;
tmp->setComponentEnvironment(_compman, -1, this);
functN[i] = tmp->getNoutputValues();
requireSorted += tmp->getRequireSorted();
nFunctValues += functN[i];
functObj[i] = tmp;
//functTp[i] = strdup(fname);
} else {
SMILE_ERR(1,"(inst '%s') Functional object '%s' specified in 'functionalsEnabled' array, however no type 'cFunctional%s' exists!",getInstName(),fname,fname);
functObj[i] = NULL;
functN[i] = 0;
free(tpname);
return 0;
//functTp[i] = NULL;
}
free(tpname);
}
if (requireSorted)
SMILE_DBG(2,"%i Functional components require sorted data.",requireSorted);
return cVectorProcessor::myConfigureInstance();
}
void set_onfo_params(DICT_WORD *intra_dict,int num_intra_dict,
char *fun_key,char *file_name,int jmol_typ,
MDCLATOMS_INFO *clatoms_info,MDATOM_MAPS *atommaps,
MDONFO *onfo,NULL_INTER_PARSE *null_inter_parse,
BUILD_INTRA *build_intra, int iresidue, int ires_off)
/*==========================================================================*/
{/*begin routine */
int num,index,ifound,igo;
int itype1,itype2;
int iatm_ind1,iatm_ind2;
int imask1,imask2;
int i,itype;
/*=======================================================================*/
/* I) Check for missing key words*/
for(i=1;i<=2;i++){
if(intra_dict[i].iuset==0 && intra_dict[i].key_type==1){
keyword_miss(intra_dict,file_name,fun_key,i);}
} /*endfor*/
/*=======================================================================*/
/* II) Fill the dictionary with words */
/*-----------------------------------------------------------------------*/
/* 1) \atom1{} */
index = 1;
sscanf(intra_dict[1].keyarg,"%d",&num);
iatm_ind1 = num;
if(iatm_ind1>build_intra->natmind_1res_now||iatm_ind1<0){
keyarg_barf(intra_dict,file_name,fun_key,index);}
imask1 = build_intra->mask_atm[iatm_ind1];
if(imask1>0)iatm_ind1 = build_intra->index_atm[iatm_ind1];
/*------------------------------------------------------------------------*/
/* 2) \atom2{} */
index = 2;
sscanf(intra_dict[2].keyarg,"%d",&num);
iatm_ind2 = num;
if(iatm_ind2>build_intra->natmind_1res_now||iatm_ind2<0){
keyarg_barf(intra_dict,file_name,fun_key,index);}
imask2 = build_intra->mask_atm[iatm_ind2];
if(imask2>0)iatm_ind2 = build_intra->index_atm[iatm_ind2];
/*-----------------------------------------------------------------------*/
/* 5) \modifier{} */
index = 5;
ifound = 0;
if(strcasecmp(intra_dict[5].keyarg,"on")==0) {ifound = 1;}
if(strcasecmp(intra_dict[5].keyarg,"off")==0){ifound = 2;}
if(ifound==0){
keyarg_barf(intra_dict,file_name,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 6) bond type */
igo = imask1*imask2;
if(igo==1){
itype1 = atommaps->iatm_atm_typ[(clatoms_info->natm_tot+iatm_ind1)];
itype2 = atommaps->iatm_atm_typ[(clatoms_info->natm_tot+iatm_ind2)];
strcpy(build_intra->confo_typ_now->atm1,atommaps->atm_typ[itype1]);
strcpy(build_intra->confo_typ_now->atm2,atommaps->atm_typ[itype2]);
strcpy(build_intra->confo_typ_now->label,intra_dict[6].keyarg);
}/*endif*/
/*======================================================================*/
/* III) Spread onfos */
if(ifound==1&&igo==1){
/*---------------------------------------------------------------------*/
/* A) Add more space */
if(onfo->num+1 > build_intra->nonfo_max){
build_intra->nonfo_max += NMEM_MIN;
onfo->j1 =(int *) crealloc(&(onfo->j1)[1],
build_intra->nonfo_max*sizeof(int),"set_onfo_params")-1;
onfo->j2 =(int *) crealloc(&(onfo->j2)[1],
build_intra->nonfo_max*sizeof(int),"set_onfo_params")-1;
onfo->jtyp =(int *) crealloc(&(onfo->jtyp)[1],
build_intra->nonfo_max*sizeof(int),"set_onfo_params")-1;
}/*endif*/
/*--------------------------------------------------------------------*/
/* C) Check type */
itype = (onfo->ntyp)+1;
for(i=1;i<=onfo->ntyp;i++){
if((strcasecmp(build_intra->confo_typ[i].atm1,
build_intra->confo_typ_now->atm1)==0)
&&(strcasecmp(build_intra->confo_typ[i].atm2,
build_intra->confo_typ_now->atm2)==0)
&&(strcasecmp(build_intra->confo_typ[i].label,
build_intra->confo_typ_now->label)==0)) {itype=i;}
if((strcasecmp(build_intra->confo_typ[i].atm1,
build_intra->confo_typ_now->atm2)==0)
&&(strcasecmp(build_intra->confo_typ[i].atm2,
build_intra->confo_typ_now->atm1)==0)
&&(strcasecmp(build_intra->confo_typ[i].label,
build_intra->confo_typ_now->label)==0)) {itype=i;}
}/*endfor*/
/*---------------------------------------------------------------------*/
/* D) Add space */
if(itype>build_intra->nonfo_typ_max){
build_intra->nonfo_typ_max += NMEM_MIN;
build_intra->confo_typ = (CBOND *)
crealloc(&(build_intra->confo_typ)[1],
build_intra->nonfo_typ_max*sizeof(CBOND),"set_onfo_params")-1;
}/*endif*/
/*---------------------------------------------------------------------*/
/* E) Add a type */
if(itype==(onfo->ntyp)+1){
onfo->ntyp+=1;
strcpy(build_intra->confo_typ[itype].atm1,
build_intra->confo_typ_now->atm1);
strcpy(build_intra->confo_typ[itype].atm2,
build_intra->confo_typ_now->atm2);
strcpy(build_intra->confo_typ[itype].label,
build_intra->confo_typ_now->label);
}/*endif*/
/*---------------------------------------------------------------------*/
/* B) Spread */
onfo->num += 1;
onfo->j1[onfo->num] = iatm_ind1 + clatoms_info->natm_tot;
onfo->j2[onfo->num] = iatm_ind2 + clatoms_info->natm_tot;
onfo->jtyp[onfo->num] = itype;
}/*endif*/
/*======================================================================*/
/* V) Spread nul onfos */
if(ifound==3&&igo==1){
/*--------------------------------------------------------------------*/
/* A) Add more space */
if(null_inter_parse->nonfo_nul+1 > build_intra->nonfo_nul_max){
build_intra->nonfo_nul_max += NMEM_MIN;
null_inter_parse->jonfo1_nul =
(int *) crealloc(&(null_inter_parse->jonfo1_nul)[1],
build_intra->nonfo_nul_max*sizeof(int),"set_onfo_params")-1;
null_inter_parse->jonfo2_nul =
(int *) crealloc(&(null_inter_parse->jonfo2_nul)[1],
build_intra->nonfo_nul_max*sizeof(int),"set_onfo_params")-1;
}/*endif*/
/*--------------------------------------------------------------------*/
/* B) Spread */
null_inter_parse->nonfo_nul += 1;
null_inter_parse->jonfo1_nul[null_inter_parse->nonfo_nul]
= iatm_ind1 + clatoms_info->natm_tot;
null_inter_parse->jonfo2_nul[null_inter_parse->nonfo_nul]
= iatm_ind2 + clatoms_info->natm_tot;
}/*endif*/
/*----------------------------------------------------------------------*/
}/*end routine*/
void set_ghost(MDGHOST_ATOMS *ghost_atoms,MDCLATOMS_INFO *clatoms_info,
MDATOM_MAPS *atommaps,BUILD_INTRA *build_intra,
DICT_WORD *atm_dict,int num_atm_dict,
char *filename,char *fun_key,int iatm_ind)
/*==========================================================================*/
{ /*begin routine*/
/*==========================================================================*/
/* Local Variables */
int nstrip=NCOEF_GHOST_MAX,imask;
int numg[NCOEF_GHOST_MAX1],index,i;
double anumg[NCOEF_GHOST_MAX1];
int nghost_old,ncomp_old,nghost;
int nghost_new,ncomp_new,ncomp,iii;
/*==========================================================================*/
/* I) Strip out indices of Ghost atoms */
ncomp = 0;index=16; /*INDEX for GHOST*/
for(i=1;i<=nstrip;i++){
if(atm_dict[index].iuset==0){break;}
ncomp = i;
strcpy(build_intra->strip1,atm_dict[index].keyarg);
parse_ghost(build_intra->strip1,build_intra->strip2,&numg[i],&anumg[i]);
index++;
}/*endfor*/
/*==========================================================================*/
/* II) Check Mask of indices making up Ghost atoms and rejigger them*/
index = 16;
for(i=1;i<=ncomp;i++){
if((numg[i]<=0)||(numg[i]>build_intra->natmind_1res_now)){
keyarg_barf(atm_dict,filename,fun_key,index);}
imask = build_intra->mask_atm[numg[i]];
if(imask==0){
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
PRINTF("You have managed to nuke one of the atoms making \n");
PRINTF("up a ghost atom without nuking the ghost atom, \n");
PRINTF("itself, in residue file %s\n",filename);
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
FFLUSH(stdout);
EXIT(1);
}/*endif*/
numg[i] = build_intra->index_atm[numg[i]];
if(numg[i]>build_intra->natm_1res_now||numg[i]<0){
keyarg_barf(atm_dict,filename,fun_key,index);}
numg[i] += clatoms_info->natm_tot;
index++;
}/*endfor*/
/*==========================================================================*/
/* III) Memory allocation */
if(ncomp>0){
ghost_atoms->nghost_tot++;
build_intra->nghost_now++;
nghost = ghost_atoms->nghost_tot;
if(nghost > build_intra->nghost_tot_max){
nghost_old = build_intra->nghost_tot_max;
ncomp_old = NCOEF_GHOST_MAX;
build_intra->nghost_tot_max+=NMEM_MIN;
nghost_new = build_intra->nghost_tot_max;
ncomp_new = NCOEF_GHOST_MAX;
ghost_atoms->ighost_map = (int *) crealloc(
&(ghost_atoms->ighost_map)[1],nghost_new*sizeof(int),"set_ghost")-1;
ghost_atoms->natm_comp = (int *) crealloc(
&(ghost_atoms->natm_comp)[1],nghost_new*sizeof(int),"set_ghost")-1;
ghost_atoms->ighost_map = (int *) crealloc(
&(ghost_atoms->ighost_map)[1],nghost_new*sizeof(int),"set_ghost")-1;
ghost_atoms->iatm_comp = creall_int_mat(ghost_atoms->iatm_comp,
1,ncomp_old,1,nghost_old,
1,ncomp_new,1,nghost_new,"set_ghost");
ghost_atoms->coef = creall_mat(ghost_atoms->coef,
1,ncomp_old,1,nghost_old,
1,ncomp_new,1,nghost_new,"set_ghost");
}/*endif*/
}/*endif*/
if(ncomp>NCOEF_GHOST_MAX){
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
PRINTF("You have managed to use too many ghost_defs!!!\n");
PRINTF("Technical support was too tired to do the \n");
PRINTF("heinous work necessary to support an arbitray number.\n");
PRINTF("Wait for the next upgrade you power tool. \n");
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
FFLUSH(stdout);
EXIT(1);
}/*endif*/
/*==========================================================================*/
/* IV) Assign Ghosts parameters */
if(ncomp>0){
ghost_atoms->ighost_flag[iatm_ind] = nghost;
ghost_atoms->natm_comp_max = MAX(ghost_atoms->natm_comp_max,ncomp);
ghost_atoms->ighost_map[nghost] = iatm_ind;
ghost_atoms->natm_comp[nghost] = ncomp;
for(i=1;i<=ncomp;i++){
ghost_atoms->iatm_comp[i][nghost] = numg[i];
ghost_atoms->coef[i][nghost] = anumg[i];
}/*endfor*/
}/*endif*/
/*--------------------------------------------------------------------------*/
}/*end routine */
void reallocate_intra_list(CLATOMS_INFO *clatoms_info,GHOST_ATOMS *ghost_atoms,
ATOMMAPS *atommaps,
BUILD_INTRA *build_intra,BONDED *bonded,
NULL_INTER_PARSE *null_inter_parse,
int jmol_typ,
int nbond_pow_add,int nbond_con_add,int nbond_null_add,
int nbend_pow_add,int nbend_con_add,int nbend_null_add,
int ntors_pow_add,int ntors_con_add,int ntors_null_add,
int nonfo_add,int nonfo_null_add,int nbend_bnd_add,
int natm_add,int nghost_add,int nfreeze_add,int ngrp_43_add,
int ngrp_33_add,int ngrp_watt_33_add,int ngrp_21_add,
int ngrp_23_add,int ngrp_46_add)
/*==========================================================================*/
/* Begin routine */
{ /*begin routine */
/*==========================================================================*/
int nmol,nmol1,mem_add_now,iii;
int nfreeze_old,nfreeze_new;
int nghost_new,nghost_old,ncomp_new,ncomp_old;
/*==========================================================================*/
/* I) Reallocate the atoms */
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*natm_add;
if(clatoms_info->natm_tot+nmol1 > build_intra->natm_tot_max){
mem_add_now = clatoms_info->natm_tot+nmol1 - build_intra->natm_tot_max;
build_intra->natm_tot_max += MAX(mem_add_now,NMEM_MIN);
clatoms_info->mass = (double *)crealloc(&((clatoms_info->mass[1])),
build_intra->natm_tot_max*
sizeof(double))-1;
clatoms_info->q = (double *)crealloc(&((clatoms_info->q[1])),
build_intra->natm_tot_max*
sizeof(double))-1;
clatoms_info->cp_vlnc_up = (int *)crealloc(&((clatoms_info->cp_vlnc_up[1])),
build_intra->natm_tot_max*
sizeof(int))-1;
clatoms_info->cp_vlnc_dn = (int *)crealloc(&((clatoms_info->cp_vlnc_dn[1])),
build_intra->natm_tot_max*
sizeof(int))-1;
clatoms_info->cp_atm_flag = (int *)crealloc(&((clatoms_info->cp_atm_flag[1])),
build_intra->natm_tot_max*
sizeof(int))-1;
clatoms_info->alp_pol = (double *)crealloc(&((clatoms_info->alp_pol[1])),
build_intra->natm_tot_max*
sizeof(double))-1;
clatoms_info->b_neut = (double *)crealloc(&((clatoms_info->b_neut[1])),
build_intra->natm_tot_max*
sizeof(double))-1;
clatoms_info->text_atm =(double *)crealloc(&((clatoms_info->text_atm[1])),
build_intra->natm_tot_max*
sizeof(double))-1;
atommaps->iatm_mol_typ = (int *) crealloc(&(atommaps->iatm_mol_typ[1]),
build_intra->natm_tot_max*
sizeof(int))-1;
atommaps->iatm_atm_typ = (int *) crealloc(&(atommaps->iatm_atm_typ[1]),
build_intra->natm_tot_max*
sizeof(int))-1;
atommaps->iatm_res_typ = (int *) crealloc(&(atommaps->iatm_res_typ[1]),
build_intra->natm_tot_max*
sizeof(int))-1;
atommaps->iatm_mol_num = (int *) crealloc(&(atommaps->iatm_mol_num[1]),
build_intra->natm_tot_max*
sizeof(int))-1;
atommaps->iatm_res_num = (int *) crealloc(&(atommaps->iatm_res_num[1]),
build_intra->natm_tot_max*
sizeof(int))-1;
atommaps->ighost_flag = (int *)crealloc(&(atommaps->ighost_flag[1]),
build_intra->natm_tot_max*
sizeof(int))-1;
atommaps->freeze_flag = (int *)crealloc(&(atommaps->freeze_flag[1]),
build_intra->natm_tot_max*
sizeof(int))-1;
atommaps->atom_label = (int *)crealloc(&(atommaps->atom_label[1]),
build_intra->natm_tot_max*
sizeof(int))-1;
}/*endif*/
/*==========================================================================*/
/* I) Reallocate the ghosts */
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*nghost_add;
if(ghost_atoms->nghost_tot+nmol1 > build_intra->nghost_tot_max){
nghost_old = build_intra->nghost_tot_max;
ncomp_old = NCOEF_GHOST_MAX;
build_intra->nghost_tot_max+=
MAX((ghost_atoms->nghost_tot+nmol1-build_intra->nghost_tot_max),NMEM_MIN);
nghost_new = build_intra->nghost_tot_max;
ncomp_new = NCOEF_GHOST_MAX;
ghost_atoms->ighost_map = (int *) crealloc(
&(ghost_atoms->ighost_map)[1],
nghost_new*sizeof(int))-1;
ghost_atoms->natm_comp = (int *) crealloc(
&(ghost_atoms->natm_comp)[1],
nghost_new*sizeof(int))-1;
ghost_atoms->iatm_comp = creall_int_mat(ghost_atoms->iatm_comp,
1,ncomp_old,1,nghost_old,
1,ncomp_new,1,nghost_new);
ghost_atoms->coef = creall_mat(ghost_atoms->coef,
1,ncomp_old,1,nghost_old,
1,ncomp_new,1,nghost_new);
}/*endif*/
/*==========================================================================*/
/* I) Reallocate the freeze */
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*nfreeze_add;
if(atommaps->nfreeze+nmol1 > build_intra->nfreeze_max){
nfreeze_old = build_intra->nfreeze_max;
build_intra->nfreeze_max+=
MAX((atommaps->nfreeze+nmol1-build_intra->nfreeze_max),NMEM_MIN);
nfreeze_new = build_intra->nfreeze_max;
atommaps->freeze_map = (int *) crealloc(
&(atommaps->freeze_map)[1],
nfreeze_new*sizeof(int))-1;
}/*endif*/
/*==========================================================================*/
/* I) Reallocate the grpcons */
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*ngrp_21_add;
if(bonded->grp_bond_con.num_21+nmol1 > build_intra->ngrp_21_max){
build_intra->ngrp_21_max +=
MAX((bonded->grp_bond_con.num_21+nmol1-build_intra->ngrp_21_max),NMEM_MIN);
bonded->grp_bond_con.j1_21 =
(int *) crealloc(&(bonded->grp_bond_con.j1_21)[1],
build_intra->ngrp_21_max*sizeof(int))-1;
bonded->grp_bond_con.j2_21 =
(int *) crealloc(&(bonded->grp_bond_con.j2_21)[1],
build_intra->ngrp_21_max*sizeof(int))-1;
bonded->grp_bond_con.jtyp_21 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_21)[1],
build_intra->ngrp_21_max*sizeof(int))-1;
}/*endif*/
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*ngrp_23_add;
if(bonded->grp_bond_con.num_23+nmol1 > build_intra->ngrp_23_max){
build_intra->ngrp_23_max +=
MAX((bonded->grp_bond_con.num_23+nmol1-build_intra->ngrp_23_max),NMEM_MIN);
bonded->grp_bond_con.j1_23 =
(int *) crealloc(&(bonded->grp_bond_con.j1_23)[1],
build_intra->ngrp_23_max*sizeof(int))-1;
bonded->grp_bond_con.j2_23 =
(int *) crealloc(&(bonded->grp_bond_con.j2_23)[1],
build_intra->ngrp_23_max*sizeof(int))-1;
bonded->grp_bond_con.j3_23 =
(int *) crealloc(&(bonded->grp_bond_con.j3_23)[1],
build_intra->ngrp_23_max*sizeof(int))-1;
bonded->grp_bond_con.jtyp_23 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_23)[1],
build_intra->ngrp_23_max*sizeof(int))-1;
}/*endif*/
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*ngrp_33_add;
if(bonded->grp_bond_con.num_33+nmol1 > build_intra->ngrp_33_max){
build_intra->ngrp_33_max +=
MAX((bonded->grp_bond_con.num_33+nmol1-build_intra->ngrp_33_max),NMEM_MIN);
bonded->grp_bond_con.j1_33 =
(int *) crealloc(&(bonded->grp_bond_con.j1_33)[1],
build_intra->ngrp_33_max*sizeof(int))-1;
bonded->grp_bond_con.j2_33 =
(int *) crealloc(&(bonded->grp_bond_con.j2_33)[1],
build_intra->ngrp_33_max*sizeof(int))-1;
bonded->grp_bond_con.j3_33 =
(int *) crealloc(&(bonded->grp_bond_con.j3_33)[1],
build_intra->ngrp_33_max*sizeof(int))-1;
bonded->grp_bond_con.jtyp_33 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_33)[1],
build_intra->ngrp_33_max*sizeof(int))-1;
}/*endif*/
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*ngrp_watt_33_add;
if(bonded->grp_bond_watts.num_33+nmol1 > build_intra->ngrp_watt_33_max){
build_intra->ngrp_watt_33_max +=
MAX((bonded->grp_bond_watts.num_33+nmol1-build_intra->ngrp_watt_33_max),
NMEM_MIN);
bonded->grp_bond_watts.j1_33 =
(int *) crealloc(&(bonded->grp_bond_watts.j1_33)[1],
build_intra->ngrp_watt_33_max*sizeof(int))-1;
bonded->grp_bond_watts.j2_33 =
(int *) crealloc(&(bonded->grp_bond_watts.j2_33)[1],
build_intra->ngrp_watt_33_max*sizeof(int))-1;
bonded->grp_bond_watts.j3_33 =
(int *) crealloc(&(bonded->grp_bond_watts.j3_33)[1],
build_intra->ngrp_watt_33_max*sizeof(int))-1;
bonded->grp_bond_watts.jtyp_33 =
(int *) crealloc(&(bonded->grp_bond_watts.jtyp_33)[1],
build_intra->ngrp_watt_33_max*sizeof(int))-1;
}/*endif*/
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*ngrp_43_add;
if(bonded->grp_bond_con.num_43+nmol1 > build_intra->ngrp_43_max){
build_intra->ngrp_43_max +=
MAX((bonded->grp_bond_con.num_43+nmol1-build_intra->ngrp_43_max),NMEM_MIN);
bonded->grp_bond_con.j1_43 =
(int *) crealloc(&(bonded->grp_bond_con.j1_43)[1],
build_intra->ngrp_43_max*sizeof(int))-1;
bonded->grp_bond_con.j2_43 =
(int *) crealloc(&(bonded->grp_bond_con.j2_43)[1],
build_intra->ngrp_43_max*sizeof(int))-1;
bonded->grp_bond_con.j3_43 =
(int *) crealloc(&(bonded->grp_bond_con.j3_43)[1],
build_intra->ngrp_43_max*sizeof(int))-1;
bonded->grp_bond_con.j4_43 =
(int *) crealloc(&(bonded->grp_bond_con.j4_43)[1],
build_intra->ngrp_43_max*sizeof(int))-1;
bonded->grp_bond_con.jtyp_43 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_43)[1],
build_intra->ngrp_43_max*sizeof(int))-1;
}/*endif*/
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*ngrp_46_add;
if(bonded->grp_bond_con.num_46+nmol1 > build_intra->ngrp_46_max){
build_intra->ngrp_46_max +=
MAX((bonded->grp_bond_con.num_46+nmol1-build_intra->ngrp_46_max),NMEM_MIN);
bonded->grp_bond_con.j1_46 =
(int *) crealloc(&(bonded->grp_bond_con.j1_46)[1],
build_intra->ngrp_46_max*sizeof(int))-1;
bonded->grp_bond_con.j2_46 =
(int *) crealloc(&(bonded->grp_bond_con.j2_46)[1],
build_intra->ngrp_46_max*sizeof(int))-1;
bonded->grp_bond_con.j3_46 =
(int *) crealloc(&(bonded->grp_bond_con.j3_46)[1],
build_intra->ngrp_46_max*sizeof(int))-1;
bonded->grp_bond_con.j4_46 =
(int *) crealloc(&(bonded->grp_bond_con.j4_46)[1],
build_intra->ngrp_46_max*sizeof(int))-1;
bonded->grp_bond_con.jtyp_46 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_46)[1],
build_intra->ngrp_46_max*sizeof(int))-1;
}/*endif*/
/*===========================================================================*/
/* I) Reallocate the bonds */
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*nbond_pow_add;
if(bonded->bond.npow+nmol1 > build_intra->nbond_pow_max){
build_intra->nbond_pow_max +=
MAX((bonded->bond.npow+nmol1-build_intra->nbond_pow_max),NMEM_MIN);
bonded->bond.j1_pow = (int *)crealloc(&(bonded->bond.j1_pow)[1],
build_intra->nbond_pow_max*sizeof(int))-1;
bonded->bond.j2_pow = (int *)crealloc(&(bonded->bond.j2_pow)[1],
build_intra->nbond_pow_max*sizeof(int))-1;
bonded->bond.jtyp_pow=(int *)crealloc(&(bonded->bond.jtyp_pow)[1],
build_intra->nbond_pow_max*sizeof(int))-1;
}/*endif*/
nmol1 = (nmol-1)*nbond_con_add;
if(bonded->bond.ncon+nmol1 > build_intra->nbond_con_max){
build_intra->nbond_con_max +=
MAX((bonded->bond.ncon+nmol1-build_intra->nbond_con_max),NMEM_MIN);
bonded->bond.j1_con = (int *)crealloc(&(bonded->bond.j1_con)[1],
build_intra->nbond_con_max*sizeof(int))-1;
bonded->bond.j2_con = (int *)crealloc(&(bonded->bond.j2_con)[1],
build_intra->nbond_con_max*sizeof(int))-1;
bonded->bond.jtyp_con=(int *)crealloc(&(bonded->bond.jtyp_con)[1],
build_intra->nbond_con_max*sizeof(int))-1;
}/*endif*/
nmol1 = (nmol-1)*nbond_null_add;
if((null_inter_parse->nbond_nul)+nmol1 > build_intra->nbond_nul_max) {
build_intra->nbond_nul_max +=
MAX((null_inter_parse->nbond_nul+nmol1-build_intra->nbond_nul_max),NMEM_MIN);
null_inter_parse->jbond1_nul =
(int *) crealloc(&(null_inter_parse->jbond1_nul)[1],
build_intra->nbond_nul_max*sizeof(int))-1;
null_inter_parse->jbond2_nul =
(int *) crealloc(&(null_inter_parse->jbond2_nul)[1],
build_intra->nbond_nul_max*sizeof(int))-1;
} /*endif*/
/*====================================================================*/
/* II) Reallocate the bends */
nmol1 = (nmol-1)*nbend_pow_add;
if(bonded->bend.npow+nmol1 > build_intra->nbend_pow_max){
build_intra->nbend_pow_max +=
MAX((bonded->bend.npow+nmol1-build_intra->nbend_pow_max),NMEM_MIN);
bonded->bend.j1_pow =(int*)crealloc(&(bonded->bend.j1_pow)[1],
build_intra->nbend_pow_max*sizeof(int))-1;
bonded->bend.j2_pow =(int*)crealloc(&(bonded->bend.j2_pow)[1],
build_intra->nbend_pow_max*sizeof(int))-1;
bonded->bend.j3_pow =(int*)crealloc(&(bonded->bend.j3_pow)[1],
build_intra->nbend_pow_max*sizeof(int))-1;
bonded->bend.jtyp_pow=(int*)crealloc(&(bonded->bend.jtyp_pow)[1],
build_intra->nbend_pow_max*sizeof(int))-1;
}/*endif*/
nmol1 = (nmol-1)*nbend_con_add;
if(bonded->bend.ncon+nmol1 > build_intra->nbend_con_max){
build_intra->nbend_con_max +=
MAX((bonded->bend.ncon+nmol1-build_intra->nbend_con_max),NMEM_MIN);
bonded->bend.j1_con = (int *)crealloc(&(bonded->bend.j1_con)[1],
build_intra->nbend_con_max*sizeof(int))-1;
bonded->bend.j2_con = (int *)crealloc(&(bonded->bend.j2_con)[1],
build_intra->nbend_con_max*sizeof(int))-1;
bonded->bend.jtyp_con=(int *)crealloc(&(bonded->bend.jtyp_con)[1],
build_intra->nbend_con_max*sizeof(int))-1;
}/*endif*/
nmol1 = (nmol-1)*nbend_null_add;
if(null_inter_parse->nbend_nul+nmol1 > build_intra->nbend_nul_max){
build_intra->nbend_nul_max +=
MAX((null_inter_parse->nbend_nul+nmol1-build_intra->nbend_nul_max),NMEM_MIN);
null_inter_parse->jbend1_nul =
(int *) crealloc(&(null_inter_parse->jbend1_nul)[1],
build_intra->nbend_nul_max*sizeof(int))-1;
null_inter_parse->jbend2_nul =
(int *) crealloc(&(null_inter_parse->jbend2_nul)[1],
build_intra->nbend_nul_max*sizeof(int))-1;
null_inter_parse->jbend3_nul =
(int *) crealloc(&(null_inter_parse->jbend3_nul)[1],
build_intra->nbend_nul_max*sizeof(int))-1;
} /*endif*/
/*====================================================================*/
/* IV) Reallocate the torsions */
nmol1 = (nmol-1)*ntors_pow_add;
if((bonded->tors.npow)+nmol1 > build_intra->ntors_pow_max){
build_intra->ntors_pow_max +=
MAX((bonded->tors.npow+nmol1-build_intra->ntors_pow_max),NMEM_MIN);
bonded->tors.j1_pow =(int*)crealloc(&(bonded->tors.j1_pow)[1],
build_intra->ntors_pow_max*sizeof(int))-1;
bonded->tors.j2_pow =(int*)crealloc(&(bonded->tors.j2_pow)[1],
build_intra->ntors_pow_max*sizeof(int))-1;
bonded->tors.j3_pow =(int*)crealloc(&(bonded->tors.j3_pow)[1],
build_intra->ntors_pow_max*sizeof(int))-1;
bonded->tors.j4_pow =(int*)crealloc(&(bonded->tors.j4_pow)[1],
build_intra->ntors_pow_max*sizeof(int))-1;
bonded->tors.jtyp_pow=(int*)crealloc(&(bonded->tors.jtyp_pow)[1],
build_intra->ntors_pow_max*sizeof(int))-1;
}/*endif*/
nmol1 = (nmol-1)*ntors_con_add;
if(bonded->tors.ncon+nmol1 > build_intra->ntors_con_max){
build_intra->ntors_con_max +=
MAX((bonded->tors.ncon+nmol1-build_intra->ntors_con_max),NMEM_MIN);
bonded->tors.j1_con = (int *) crealloc(&(bonded->tors.j1_con)[1],
build_intra->ntors_con_max*sizeof(int))-1;
bonded->tors.j2_con = (int *) crealloc(&(bonded->tors.j2_con)[1],
build_intra->ntors_con_max*sizeof(int))-1;
bonded->tors.j3_con = (int *) crealloc(&(bonded->tors.j3_con)[1],
build_intra->ntors_con_max*sizeof(int))-1;
bonded->tors.j4_con = (int *) crealloc(&(bonded->tors.j4_con)[1],
build_intra->ntors_con_max*sizeof(int))-1;
bonded->tors.jtyp_con=(int *) crealloc(&(bonded->tors.jtyp_con)[1],
build_intra->ntors_con_max*sizeof(int))-1;
} /* endif */
nmol1 = (nmol-1)*ntors_null_add;
if(null_inter_parse->ntors_nul+nmol1 > build_intra->ntors_nul_max){
build_intra->ntors_nul_max +=
MAX((null_inter_parse->ntors_nul+nmol1-build_intra->ntors_nul_max),NMEM_MIN);
null_inter_parse->jtors1_nul =
(int *) crealloc(&(null_inter_parse->jtors1_nul[1]),
build_intra->ntors_nul_max*sizeof(int))-1;
null_inter_parse->jtors2_nul =
(int *) crealloc(&(null_inter_parse->jtors2_nul[1]),
build_intra->ntors_nul_max*sizeof(int))-1;
null_inter_parse->jtors3_nul =
(int *) crealloc(&(null_inter_parse->jtors3_nul[1]),
build_intra->ntors_nul_max*sizeof(int))-1;
null_inter_parse->jtors4_nul =
(int *) crealloc(&(null_inter_parse->jtors4_nul[1]),
build_intra->ntors_nul_max*sizeof(int))-1;
} /*endif*/
/*====================================================================*/
/* V) Reallocate the torsions */
nmol1 = (nmol-1)*nonfo_add;
if(bonded->onfo.num+nmol1 > build_intra->nonfo_max){
build_intra->nonfo_max +=
MAX((bonded->onfo.num+nmol1-build_intra->nonfo_max),NMEM_MIN);
bonded->onfo.j1 =(int *) crealloc(&(bonded->onfo.j1)[1],
build_intra->nonfo_max*sizeof(int))-1;
bonded->onfo.j2 =(int *) crealloc(&(bonded->onfo.j2)[1],
build_intra->nonfo_max*sizeof(int))-1;
bonded->onfo.jtyp =(int *) crealloc(&(bonded->onfo.jtyp)[1],
build_intra->nonfo_max*sizeof(int))-1;
}/*endif*/
nmol1 = (nmol-1)*nonfo_null_add;
if(null_inter_parse->nonfo_nul+nmol1 > build_intra->nonfo_nul_max){
build_intra->nonfo_nul_max +=
MAX((null_inter_parse->nonfo_nul+nmol1-build_intra->nonfo_nul_max),NMEM_MIN);
null_inter_parse->jonfo1_nul =
(int *) crealloc(&(null_inter_parse->jonfo1_nul)[1],
build_intra->nonfo_nul_max*sizeof(int))-1;
null_inter_parse->jonfo2_nul =
(int *) crealloc(&(null_inter_parse->jonfo2_nul)[1],
build_intra->nonfo_nul_max*sizeof(int))-1;
}/*endif*/
/*====================================================================*/
/* VI) Reallocate the Uri-Bradleys */
nmol1 = (nmol-1)*nbend_bnd_add;
if(bonded->bend_bnd.num+nmol1 > build_intra->nbend_bnd_max){
mem_add_now = bonded->bend_bnd.num+nmol1-build_intra->nbend_bnd_max;
build_intra->nbend_bnd_max += MAX(mem_add_now,NMEM_MIN);
bonded->bend_bnd.j1 =(int*)crealloc(&(bonded->bend_bnd.j1)[1],
build_intra->nbend_bnd_max*sizeof(int))-1;
bonded->bend_bnd.j2 =(int*)crealloc(&(bonded->bend_bnd.j2)[1],
build_intra->nbend_bnd_max*sizeof(int))-1;
bonded->bend_bnd.j3 =(int*)crealloc(&(bonded->bend_bnd.j3)[1],
build_intra->nbend_bnd_max*sizeof(int))-1;
bonded->bend_bnd.jtyp=(int*)crealloc(&(bonded->bend_bnd.jtyp)[1],
build_intra->nbend_bnd_max*sizeof(int))-1;
}/*endif*/
/*==========================================================================*/
} /*end routine*/
void change_board_size(struct board *src_board, int new_width, int new_height)
{
int board_width = src_board->board_width;
int board_height = src_board->board_height;
if(new_width == 0)
new_width = 1;
if(new_height == 0)
new_height = 1;
if((board_width != new_width) || (board_height != new_height))
{
char *level_id = src_board->level_id;
char *level_color = src_board->level_color;
char *level_param = src_board->level_param;
char *level_under_id = src_board->level_under_id;
char *level_under_color = src_board->level_under_color;
char *level_under_param = src_board->level_under_param;
char *overlay = src_board->overlay;
char *overlay_color = src_board->overlay_color;
int overlay_mode = src_board->overlay_mode;
int board_size = board_width * board_height;
int new_size = new_width * new_height;
int i;
// Shrinking height? Remove any robots/scrolls/sensors from excess lines
if(new_height < board_height)
{
int offset;
int check_id;
for(offset = new_height * board_width; offset < board_size;
offset++)
{
check_id = level_id[offset];
if(check_id == 122)
clear_sensor_id(src_board, level_param[offset]);
else
if((check_id == 126) || (check_id == 125))
clear_scroll_id(src_board, level_param[offset]);
else
if((check_id == 123) || (check_id == 124))
clear_robot_id(src_board, level_param[offset]);
}
}
if(new_width < board_width)
{
// Take out pieces from each width, then reallocate.
// Only do this for the current height or the new height, whichever is
// less.
int src_offset, dest_offset;
int max_height = new_height;
int check_id, offset;
if(new_height > board_height)
max_height = board_height;
for(i = 0, src_offset = 0, dest_offset = 0; i < max_height;
i++, src_offset += board_width, dest_offset += new_width)
{
// First, remove any robots/scrolls/sensors from excess chunks
for(offset = src_offset + new_width; offset < src_offset + board_width;
offset++)
{
check_id = level_id[offset];
if(check_id == 122)
clear_sensor_id(src_board, level_param[offset]);
else
if((check_id == 126) || (check_id == 125))
clear_scroll_id(src_board, level_param[offset]);
else
if((check_id == 123) || (check_id == 124))
clear_robot_id(src_board, level_param[offset]);
}
memmove(level_id + dest_offset, level_id + src_offset, new_width);
memmove(level_param + dest_offset, level_param + src_offset, new_width);
memmove(level_color + dest_offset, level_color + src_offset, new_width);
memmove(level_under_id + dest_offset,
level_under_id + src_offset, new_width);
memmove(level_under_param + dest_offset,
level_under_param + src_offset, new_width);
memmove(level_under_color + dest_offset,
level_under_color + src_offset, new_width);
}
// Resize layers
src_board->level_id = crealloc(level_id, new_size);
src_board->level_color = crealloc(level_color, new_size);
src_board->level_param = crealloc(level_param, new_size);
src_board->level_under_id = crealloc(level_under_id, new_size);
src_board->level_under_color = crealloc(level_under_color, new_size);
src_board->level_under_param = crealloc(level_under_param, new_size);
level_id = src_board->level_id;
level_color = src_board->level_color;
level_param = src_board->level_param;
level_under_id = src_board->level_under_id;
level_under_color = src_board->level_under_color;
level_under_param = src_board->level_under_param;
// Do the overlay too, if it exists
if(overlay_mode)
{
for(i = 0, src_offset = 0, dest_offset = 0; i < max_height;
i++, src_offset += board_width, dest_offset += new_width)
{
memmove(overlay + dest_offset, overlay + src_offset, new_width);
memmove(overlay_color + dest_offset, overlay_color + src_offset, new_width);
}
src_board->overlay = crealloc(overlay, new_size);
src_board->overlay_color = crealloc(overlay_color, new_size);
overlay = src_board->overlay;
overlay_color = src_board->overlay_color;
}
}
else
if(new_width > board_width)
{
// Reallocate first, then copy over pieces, padding in widths
// Only do this for the current height or the new height, whichever is
// less.
int src_offset, dest_offset;
int max_height = new_height;
int width_difference = new_width - board_width;
if(new_height > board_height)
max_height = board_height;
// Resize first this time.
src_board->level_id = crealloc(level_id, new_size);
src_board->level_color = crealloc(level_color, new_size);
src_board->level_param = crealloc(level_param, new_size);
src_board->level_under_id = crealloc(level_under_id, new_size);
src_board->level_under_color = crealloc(level_under_color, new_size);
src_board->level_under_param = crealloc(level_under_param, new_size);
// Resize the overlay too, if it exists
if(overlay_mode)
{
src_board->overlay = crealloc(overlay, new_size);
src_board->overlay_color = crealloc(overlay_color, new_size);
overlay = src_board->overlay;
overlay_color = src_board->overlay_color;
}
level_id = src_board->level_id;
level_color = src_board->level_color;
level_param = src_board->level_param;
level_under_id = src_board->level_under_id;
level_under_color = src_board->level_under_color;
level_under_param = src_board->level_under_param;
// And start at the end instead of the beginning
src_offset = board_width * (max_height - 1);
dest_offset = new_width * (max_height - 1);
for(i = 0; i < max_height; i++, src_offset -= board_width, dest_offset -= new_width)
{
memmove(level_id + dest_offset, level_id + src_offset, board_width);
memmove(level_param + dest_offset, level_param + src_offset, board_width);
memmove(level_color + dest_offset, level_color + src_offset, board_width);
memmove(level_under_id + dest_offset,
level_under_id + src_offset, board_width);
memmove(level_under_param + dest_offset,
level_under_param + src_offset, board_width);
memmove(level_under_color + dest_offset,
level_under_color + src_offset, board_width);
// And fill in the remainder with blanks
memset(level_id + dest_offset + board_width, 0, width_difference);
memset(level_param + dest_offset + board_width, 0, width_difference);
memset(level_color + dest_offset + board_width, 7, width_difference);
memset(level_under_id + dest_offset + board_width, 0, width_difference);
memset(level_under_param + dest_offset + board_width, 0, width_difference);
memset(level_under_color + dest_offset + board_width, 7, width_difference);
}
src_offset = board_width * (max_height - 1);
dest_offset = new_width * (max_height - 1);
// Do the overlay too, if it exists
if(overlay_mode)
{
for(i = 0; i < max_height; i++, src_offset -= board_width, dest_offset -= new_width)
{
memmove(overlay + dest_offset, overlay + src_offset, board_width);
memmove(overlay_color + dest_offset, overlay_color + src_offset, board_width);
// And fill in the remainder with blanks
memset(overlay + dest_offset + board_width, 32, width_difference);
memset(overlay_color + dest_offset + board_width, 7, width_difference);
}
}
}
else
{
// Width remains the same, just a straight resize
src_board->level_id = crealloc(level_id, new_size);
src_board->level_color = crealloc(level_color, new_size);
src_board->level_param = crealloc(level_param, new_size);
src_board->level_under_id = crealloc(level_under_id, new_size);
src_board->level_under_color = crealloc(level_under_color, new_size);
src_board->level_under_param = crealloc(level_under_param, new_size);
// Resize the overlay too, if it exists
if(overlay_mode)
{
src_board->overlay = crealloc(overlay, new_size);
src_board->overlay_color = crealloc(overlay_color, new_size);
}
level_id = src_board->level_id;
level_color = src_board->level_color;
level_param = src_board->level_param;
level_under_id = src_board->level_under_id;
level_under_color = src_board->level_under_color;
level_under_param = src_board->level_under_param;
overlay = src_board->overlay;
overlay_color = src_board->overlay_color;
}
// Fill in any blanks
if(new_height > board_height)
{
int offset = new_width * board_height;
int size_difference = new_size - offset;
memset(level_id + offset, 0, size_difference);
memset(level_param + offset, 0, size_difference);
memset(level_color + offset, 7, size_difference);
memset(level_under_id + offset, 0, size_difference);
memset(level_under_param + offset, 0, size_difference);
memset(level_under_color + offset, 7, size_difference);
if(overlay_mode)
{
memset(overlay + offset, 32, size_difference);
memset(overlay_color + offset, 7, size_difference);
}
}
// Set the new sizes
src_board->board_width = new_width;
src_board->board_height = new_height;
}
}
__editor_maybe_static void load_board_direct(struct board *cur_board,
FILE *fp, int savegame, int version)
{
int num_robots, num_scrolls, num_sensors, num_robots_active;
int overlay_mode, size, board_width, board_height, i;
struct robot *cur_robot;
struct scroll *cur_scroll;
struct sensor *cur_sensor;
char *test_buffer;
// Initialize some fields that may no longer be loaded
// from the board file itself..
cur_board->last_key = '?';
cur_board->num_input = 0;
cur_board->input_size = 0;
cur_board->input_string[0] = 0;
cur_board->player_last_dir = 0x10;
cur_board->bottom_mesg[0] = 0;
cur_board->b_mesg_timer = 0;
cur_board->lazwall_start = 7;
cur_board->b_mesg_row = 24;
cur_board->b_mesg_col = -1;
cur_board->scroll_x = 0;
cur_board->scroll_y = 0;
cur_board->locked_x = -1;
cur_board->locked_y = -1;
cur_board->volume = 255;
cur_board->volume_inc = 0;
cur_board->volume_target = 255;
// board_mode, unused
fgetc(fp);
overlay_mode = fgetc(fp);
if(!overlay_mode)
{
int overlay_width;
int overlay_height;
overlay_mode = fgetc(fp);
overlay_width = fgetw(fp);
overlay_height = fgetw(fp);
size = overlay_width * overlay_height;
cur_board->overlay = cmalloc(size);
cur_board->overlay_color = cmalloc(size);
load_RLE2_plane(cur_board->overlay, fp, size);
test_buffer = cmalloc(1024);
free(test_buffer);
// Skip sizes
fseek(fp, 4, SEEK_CUR);
load_RLE2_plane(cur_board->overlay_color, fp, size);
test_buffer = cmalloc(1024);
free(test_buffer);
}
else
{
overlay_mode = 0;
// Undo that last get
fseek(fp, -1, SEEK_CUR);
}
cur_board->overlay_mode = overlay_mode;
board_width = fgetw(fp);
board_height = fgetw(fp);
cur_board->board_width = board_width;
cur_board->board_height = board_height;
size = board_width * board_height;
cur_board->level_id = cmalloc(size);
cur_board->level_color = cmalloc(size);
cur_board->level_param = cmalloc(size);
cur_board->level_under_id = cmalloc(size);
cur_board->level_under_color = cmalloc(size);
cur_board->level_under_param = cmalloc(size);
load_RLE2_plane(cur_board->level_id, fp, size);
fseek(fp, 4, SEEK_CUR);
load_RLE2_plane(cur_board->level_color, fp, size);
fseek(fp, 4, SEEK_CUR);
load_RLE2_plane(cur_board->level_param, fp, size);
fseek(fp, 4, SEEK_CUR);
load_RLE2_plane(cur_board->level_under_id, fp, size);
fseek(fp, 4, SEEK_CUR);
load_RLE2_plane(cur_board->level_under_color, fp, size);
fseek(fp, 4, SEEK_CUR);
load_RLE2_plane(cur_board->level_under_param, fp, size);
// Load board parameters
if(version < 0x0253)
{
fread(cur_board->mod_playing, LEGACY_MOD_FILENAME_MAX, 1, fp);
cur_board->mod_playing[LEGACY_MOD_FILENAME_MAX] = 0;
}
else
{
size_t len = fgetw(fp);
if(len >= MAX_PATH)
len = MAX_PATH - 1;
fread(cur_board->mod_playing, len, 1, fp);
cur_board->mod_playing[len] = 0;
}
cur_board->viewport_x = fgetc(fp);
cur_board->viewport_y = fgetc(fp);
cur_board->viewport_width = fgetc(fp);
cur_board->viewport_height = fgetc(fp);
cur_board->can_shoot = fgetc(fp);
cur_board->can_bomb = fgetc(fp);
cur_board->fire_burn_brown = fgetc(fp);
cur_board->fire_burn_space = fgetc(fp);
cur_board->fire_burn_fakes = fgetc(fp);
cur_board->fire_burn_trees = fgetc(fp);
cur_board->explosions_leave = fgetc(fp);
cur_board->save_mode = fgetc(fp);
cur_board->forest_becomes = fgetc(fp);
cur_board->collect_bombs = fgetc(fp);
cur_board->fire_burns = fgetc(fp);
for(i = 0; i < 4; i++)
{
cur_board->board_dir[i] = fgetc(fp);
}
cur_board->restart_if_zapped = fgetc(fp);
cur_board->time_limit = fgetw(fp);
if(version < 0x0253)
{
cur_board->last_key = fgetc(fp);
cur_board->num_input = fgetw(fp);
cur_board->input_size = fgetc(fp);
fread(cur_board->input_string, LEGACY_INPUT_STRING_MAX + 1, 1, fp);
cur_board->input_string[LEGACY_INPUT_STRING_MAX] = 0;
cur_board->player_last_dir = fgetc(fp);
fread(cur_board->bottom_mesg, LEGACY_BOTTOM_MESG_MAX + 1, 1, fp);
cur_board->bottom_mesg[LEGACY_BOTTOM_MESG_MAX] = 0;
cur_board->b_mesg_timer = fgetc(fp);
cur_board->lazwall_start = fgetc(fp);
cur_board->b_mesg_row = fgetc(fp);
cur_board->b_mesg_col = (signed char)fgetc(fp);
cur_board->scroll_x = (signed short)fgetw(fp);
cur_board->scroll_y = (signed short)fgetw(fp);
cur_board->locked_x = (signed short)fgetw(fp);
cur_board->locked_y = (signed short)fgetw(fp);
}
else if(savegame)
{
size_t len;
cur_board->last_key = fgetc(fp);
cur_board->num_input = fgetw(fp);
cur_board->input_size = fgetw(fp);
len = fgetw(fp);
if(len >= ROBOT_MAX_TR)
len = ROBOT_MAX_TR - 1;
fread(cur_board->input_string, len, 1, fp);
cur_board->input_string[len] = 0;
cur_board->player_last_dir = fgetc(fp);
len = fgetw(fp);
if(len >= ROBOT_MAX_TR)
len = ROBOT_MAX_TR - 1;
fread(cur_board->bottom_mesg, len, 1, fp);
cur_board->bottom_mesg[len] = 0;
cur_board->b_mesg_timer = fgetc(fp);
cur_board->lazwall_start = fgetc(fp);
cur_board->b_mesg_row = fgetc(fp);
cur_board->b_mesg_col = (signed char)fgetc(fp);
cur_board->scroll_x = (signed short)fgetw(fp);
cur_board->scroll_y = (signed short)fgetw(fp);
cur_board->locked_x = (signed short)fgetw(fp);
cur_board->locked_y = (signed short)fgetw(fp);
}
cur_board->player_ns_locked = fgetc(fp);
cur_board->player_ew_locked = fgetc(fp);
cur_board->player_attack_locked = fgetc(fp);
if(version < 0x0253 || savegame)
{
cur_board->volume = fgetc(fp);
cur_board->volume_inc = fgetc(fp);
cur_board->volume_target = fgetc(fp);
}
// Load robots
num_robots = fgetc(fp);
num_robots_active = 0;
cur_board->robot_list = ccalloc(num_robots + 1, sizeof(struct robot *));
// Also allocate for name sorted list
cur_board->robot_list_name_sorted =
ccalloc(num_robots, sizeof(struct robot *));
// Any null objects being placed will later be optimized out
if(num_robots)
{
for(i = 1; i <= num_robots; i++)
{
cur_robot = load_robot_allocate(fp, savegame, version);
if(cur_robot->used)
{
cur_board->robot_list[i] = cur_robot;
cur_board->robot_list_name_sorted[num_robots_active] = cur_robot;
num_robots_active++;
}
else
{
// We don't need no null robot
clear_robot(cur_robot);
cur_board->robot_list[i] = NULL;
}
}
}
if(num_robots_active)
{
if(num_robots_active != num_robots)
{
cur_board->robot_list_name_sorted =
crealloc(cur_board->robot_list_name_sorted,
sizeof(struct robot *) * num_robots_active);
}
qsort(cur_board->robot_list_name_sorted, num_robots_active,
sizeof(struct robot *), cmp_robots);
}
else
{
free(cur_board->robot_list_name_sorted);
cur_board->robot_list_name_sorted = NULL;
}
cur_board->num_robots = num_robots;
cur_board->num_robots_allocated = num_robots;
cur_board->num_robots_active = num_robots_active;
// Load scrolls
num_scrolls = fgetc(fp);
cur_board->scroll_list = ccalloc(num_scrolls + 1, sizeof(struct scroll *));
if(num_scrolls)
{
for(i = 1; i <= num_scrolls; i++)
{
cur_scroll = load_scroll_allocate(fp);
if(cur_scroll->used)
cur_board->scroll_list[i] = cur_scroll;
else
clear_scroll(cur_scroll);
}
}
cur_board->num_scrolls = num_scrolls;
cur_board->num_scrolls_allocated = num_scrolls;
// Load sensors
num_sensors = fgetc(fp);
cur_board->sensor_list = ccalloc(num_sensors + 1, sizeof(struct sensor *));
if(num_sensors)
{
for(i = 1; i <= num_sensors; i++)
{
cur_sensor = load_sensor_allocate(fp);
if(cur_sensor->used)
cur_board->sensor_list[i] = cur_sensor;
else
clear_sensor(cur_sensor);
}
}
cur_board->num_sensors = num_sensors;
cur_board->num_sensors_allocated = num_sensors;
}
void fetch_freeze(CLASS_PARSE *class_parse, ATOMMAPS *atommaps,
BUILD_INTRA *build_intra, START_INDEX *start_index,
CLATOMS_INFO *clatoms_info, int jmol_typ)
/*==========================================================================*/
/*begin routine*/{
/*==========================================================================*/
/* Define Local variable */
int i,iii,nfreeze_now,iresidue_off,nresidue,count;
int count_atm,ires;
double *mass = clatoms_info->mass;
/*==========================================================================*/
/* I) No atoms frozen */
if(class_parse->mol_freeze_opt[jmol_typ]==0){
for(i=start_index->natm+1;i<=clatoms_info->natm_tot;i++){
atommaps->freeze_flag[i] = 0;
}/*endfor*/
}/*endif*/
/*==========================================================================*/
/* II) All atoms frozen */
if(class_parse->mol_freeze_opt[jmol_typ]==1){
for(i=start_index->natm+1;i<=clatoms_info->natm_tot;i++){
atommaps->freeze_flag[i] = atommaps->nfreeze+i-start_index->natm;
}/*endfor*/
nfreeze_now = clatoms_info->natm_tot - start_index->natm;
atommaps->nfreeze += nfreeze_now;
if((atommaps->nfreeze) > build_intra->nfreeze_max){
build_intra->nfreeze_max += MAX(NMEM_MIN,nfreeze_now);
atommaps->freeze_map = (int *) crealloc(&(atommaps->freeze_map[1]),
build_intra->nfreeze_max*
sizeof(int))-1;
}/*endif*/
for(i=start_index->nfreeze+1;i<=atommaps->nfreeze;i++){
atommaps->freeze_map[i] = start_index->natm+i-start_index->nfreeze;
}/*endfor*/
/* Do the degrees of freedom for each molecule */
iresidue_off = atommaps->jres_jmol_typ_strt[jmol_typ]-1;
atommaps->nfree_1mol_jmol_typ[jmol_typ] = 0;
atommaps->icons_jmol_typ[jmol_typ] = 0;
nresidue = MAX(atommaps->nres_1mol_jmol_typ[jmol_typ],1);
for(i=1;i<=nresidue;i++){
atommaps->nfree_jres_jmol_typ[(iresidue_off+i)] = 0.0;
/*endfor*/}
}/*endif*/
/*==========================================================================*/
/* III) Backbone atoms frozen */
if(class_parse->mol_freeze_opt[jmol_typ]==2){
/* Count the freeze map and fill the freeze_flag list */
nfreeze_now = atommaps->nfreeze;
for(i=start_index->natm+1;i<=clatoms_info->natm_tot;i++){
if(atommaps->atom_label[i] == 1){
nfreeze_now++;
atommaps->freeze_flag[i] = i;
}/*endif*/
}/*endfor*/
/* Realloc the freeze map */
if(nfreeze_now > build_intra->nfreeze_max){
build_intra->nfreeze_max += MAX(NMEM_MIN,nfreeze_now-atommaps->nfreeze);
atommaps->freeze_map = (int *) crealloc(&(atommaps->freeze_map[1]),
build_intra->nfreeze_max*
sizeof(int))-1;
}/*endif*/
/* Fill the freeze map and do the degrees of freedom for each molecule */
count = 0;
count_atm = 0;
iresidue_off = atommaps->jres_jmol_typ_strt[jmol_typ]-1;
ires = iresidue_off+1;
for(i=start_index->natm+1;i<=clatoms_info->natm_tot;i++){
count_atm++;
if(count_atm > atommaps->natm_jres_jmol_typ[ires]){
count_atm = 1;
ires++;
}/*endif*/
if(atommaps->atom_label[i] == 1){
count++;
atommaps->freeze_map[(atommaps->nfreeze+count)] = i;
atommaps->nfree_1mol_jmol_typ[jmol_typ] -= 3;
atommaps->nfree_jres_jmol_typ[ires] -= 3;
}/*endif*/
}/*endfor*/
atommaps->nfreeze = nfreeze_now;
#ifdef DEBUG
for(i=1;i<=atommaps->nfreeze;i++){
printf("This is present freeze map %d\n",atommaps->freeze_map[i]);
scanf("%d",&iii);
}
printf("This is molecule degrees of freedom %d\n",
atommaps->nfree_1mol_jmol_typ[jmol_typ]);
scanf("%d",&iii);
nresidue = MAX(atommaps->nres_1mol_jmol_typ[jmol_typ],1);
for(i=1;i<=nresidue;i++){
printf("This is residue degrees of freedom %d %d\n",
atommaps->nfree_jres_jmol_typ[i+iresidue_off],i);
scanf("%d",&iii);
}
#endif
}/*endif*/
/*==========================================================================*/
/* IV) All Heavy atoms frozen */
if(class_parse->mol_freeze_opt[jmol_typ]==3){
/* Count the freeze map and fill the freeze_flag list */
nfreeze_now = atommaps->nfreeze;
for(i=start_index->natm+1;i<=clatoms_info->natm_tot;i++){
if(mass[i] > 1.5){
nfreeze_now++;
atommaps->freeze_flag[i] = i;
}/*endif*/
}/*endfor*/
/* Realloc the freeze map */
if(nfreeze_now > build_intra->nfreeze_max){
printf(" reallocing freeze_map \n");
build_intra->nfreeze_max += MAX(NMEM_MIN,nfreeze_now-atommaps->nfreeze);
atommaps->freeze_map = (int *) crealloc(&(atommaps->freeze_map[1]),
build_intra->nfreeze_max*
sizeof(int))-1;
}/*endif*/
/* Fill the freeze map and do the degrees of freedom for each molecule */
count = 0;
count_atm = 0;
iresidue_off = atommaps->jres_jmol_typ_strt[jmol_typ]-1;
ires = iresidue_off+1;
for(i=start_index->natm+1;i<=clatoms_info->natm_tot;i++){
count_atm++;
if(count_atm > atommaps->natm_jres_jmol_typ[ires]){
count_atm = 1;
ires++;
}/*endif*/
if(mass[i] > 1.5){
count++;
atommaps->freeze_map[(atommaps->nfreeze+count)] = i;
atommaps->nfree_1mol_jmol_typ[jmol_typ] -= 3;
atommaps->nfree_jres_jmol_typ[ires] -= 3;
}/*endif*/
}/*endfor*/
atommaps->nfreeze = nfreeze_now;
/* printf("nfreeze_now %d \n",nfreeze_now);
printf("exiting from fetch_freeze \n"); exit(1); */
}/*endif*/
/*--------------------------------------------------------------------------*/
}/*end routine*/
void close_intra_params(CLATOMS_INFO *clatoms_info,CLATOMS_POS *clatoms_pos,
GHOST_ATOMS *ghost_atoms,
ATOMMAPS *atommaps,
BUILD_INTRA *build_intra,
BONDED *bonded,
NULL_INTER_PARSE *null_inter_parse,
double *tot_memory,SIMOPTS *simopts,int np_forc)
/*=======================================================================*/
/* Begin routine */
{/*begin routine*/
/*=======================================================================*/
/* Local Variables */
int i,ntyp_pow,iii,nsec,inow,know;
double now_memory;
int natm_typ_mall;
int natm_mall;
int nghost_mall;
int nfreeze_mall;
int ncomp_mall;
int nchrg_mall;
int ngrp_21_mall;
int ngrp_typ_21_mall;
int ngrp_33_mall;
int ngrp_typ_33_mall;
int ngrp_watt_33_mall;
int ngrp_typ_watt_33_mall;
int ngrp_43_mall;
int ngrp_typ_43_mall;
int ngrp_23_mall;
int ngrp_typ_23_mall;
int ngrp_46_mall;
int ngrp_typ_46_mall;
int nbond_pow_mall;
int nbond_typ_pow_mall;
int nbond_con_mall;
int nbond_typ_con_mall;
int nbend_pow_mall;
int nbend_typ_pow_mall;
int nbend_con_mall;
int nbend_typ_con_mall;
int nbend_bnd_mall;
int nbend_bnd_typ_mall;
int ntors_pow_mall;
int ntors_typ_pow_mall;
int ntors_con_mall;
int ntors_typ_con_mall;
int nonfo_mall;
int nonfo_typ_mall;
int pimd_on;
int nghost_old,nfreeze_old,ncomp_old;
int pi_beads = clatoms_info->pi_beads;
int pimd_freez_typ = atommaps->pimd_freez_typ;
/*======================================================================*/
/* 0) Make the length of each vector an odd number */
nghost_old = build_intra->nghost_tot_max;
nfreeze_old = build_intra->nfreeze_max;
ncomp_old = NCOEF_GHOST_MAX;
natm_mall = clatoms_info->natm_tot;
natm_typ_mall = atommaps->natm_typ;
nghost_mall = ghost_atoms->nghost_tot;
nfreeze_mall = atommaps->nfreeze;
ncomp_mall = ghost_atoms->natm_comp_max;
ngrp_21_mall = bonded->grp_bond_con.num_21;
ngrp_33_mall = bonded->grp_bond_con.num_33;
ngrp_watt_33_mall = bonded->grp_bond_watts.num_33;
ngrp_43_mall = bonded->grp_bond_con.num_43;
ngrp_23_mall = bonded->grp_bond_con.num_23;
ngrp_46_mall = bonded->grp_bond_con.num_46;
ngrp_typ_21_mall = bonded->grp_bond_con.ntyp_21;
ngrp_typ_33_mall = bonded->grp_bond_con.ntyp_33;
ngrp_typ_watt_33_mall = bonded->grp_bond_watts.ntyp_33;
ngrp_typ_43_mall = bonded->grp_bond_con.ntyp_43;
ngrp_typ_23_mall = bonded->grp_bond_con.ntyp_23;
ngrp_typ_46_mall = bonded->grp_bond_con.ntyp_46;
nbond_pow_mall = bonded->bond.npow;
nbond_typ_pow_mall = bonded->bond.ntyp_pow;
nbond_con_mall = bonded->bond.ncon;
nbond_typ_con_mall = bonded->bond.ntyp_con;
nbend_pow_mall = bonded->bend.npow;
nbend_typ_pow_mall = bonded->bend.ntyp_pow;
nbend_con_mall = bonded->bend.ncon;
nbend_typ_con_mall = bonded->bend.ntyp_con;
nbend_bnd_mall = bonded->bend_bnd.num;
nbend_bnd_typ_mall = bonded->bend_bnd.ntyp;
ntors_pow_mall = bonded->tors.npow;
ntors_typ_pow_mall = bonded->tors.ntyp_pow;
ntors_con_mall = bonded->tors.ncon;
ntors_typ_con_mall = bonded->tors.ntyp_con;
nonfo_mall = bonded->onfo.num;
nonfo_typ_mall = bonded->onfo.ntyp;
if((natm_mall % 2)==0){natm_mall += 1;}
nsec=natm_mall/np_forc;
if((natm_mall%np_forc)!=0){nsec++;}
natm_mall = nsec*np_forc;
if((natm_typ_mall % 2)==0){natm_typ_mall += 1;}
if(((nghost_mall % 2)==0)
&&(nghost_mall !=0)){nghost_mall++;}
if(((nfreeze_mall % 2)==0)
&&(nfreeze_mall !=0)){nfreeze_mall++;}
if(((ncomp_mall % 2)==0)
&&(ncomp_mall !=0)){ncomp_mall++;}
if(((ngrp_21_mall % 2)==0)
&&(ngrp_21_mall !=0)){ngrp_21_mall++;}
if(((ngrp_33_mall % 2)==0)
&&(ngrp_33_mall !=0)){ngrp_33_mall++;}
if(((ngrp_watt_33_mall % 2)==0)
&&(ngrp_watt_33_mall !=0)){ngrp_watt_33_mall++;}
if(((ngrp_43_mall % 2)==0)
&&(ngrp_43_mall !=0)){ngrp_43_mall++;}
if(((ngrp_23_mall % 2)==0)
&&(ngrp_23_mall !=0)){ngrp_23_mall++;}
if(((ngrp_46_mall % 2)==0)
&&(ngrp_46_mall !=0)){ngrp_46_mall++;}
if(((ngrp_typ_21_mall % 2)==0)
&&(ngrp_typ_21_mall !=0)){ngrp_typ_21_mall++;}
if(((ngrp_typ_33_mall % 2)==0)
&&(ngrp_typ_33_mall !=0)){ngrp_typ_33_mall++;}
if(((ngrp_typ_watt_33_mall % 2)==0)
&&(ngrp_typ_watt_33_mall !=0)){ngrp_typ_watt_33_mall++;}
if(((ngrp_typ_43_mall % 2)==0)
&&(ngrp_typ_43_mall !=0)){ngrp_typ_43_mall++;}
if(((ngrp_typ_23_mall % 2)==0)
&&(ngrp_typ_23_mall !=0)){ngrp_typ_23_mall++;}
if(((ngrp_typ_46_mall % 2)==0)
&&(ngrp_typ_46_mall !=0)){ngrp_typ_46_mall++;}
if(((nbond_pow_mall % 2)==0)
&&(nbond_pow_mall !=0)){nbond_pow_mall += 1;}
if(((nbond_typ_pow_mall % 2)==0)
&&(nbond_typ_pow_mall !=0)){nbond_typ_pow_mall+= 1;}
if(((nbond_con_mall % 2)==0)
&&(nbond_con_mall !=0)){nbond_pow_mall += 1;}
if(((nbond_typ_con_mall % 2)==0)
&&(nbond_typ_con_mall !=0)){nbond_typ_pow_mall+= 1;}
if(((nbend_pow_mall % 2)==0)
&&(nbend_pow_mall !=0)){nbend_pow_mall += 1;}
if(((nbend_typ_pow_mall % 2)==0)
&&(nbend_typ_pow_mall !=0)){nbend_typ_pow_mall+= 1;}
if(((nbend_con_mall % 2)==0)
&&(nbend_con_mall !=0)){nbend_pow_mall += 1;}
if(((nbend_typ_con_mall % 2)==0)
&&(nbend_typ_con_mall !=0)){nbend_typ_pow_mall+= 1;}
if(((nbend_bnd_mall % 2)==0)
&&(nbend_bnd_mall !=0)){nbend_bnd_mall += 1;}
if(((nbend_bnd_typ_mall % 2)==0)
&&(nbend_bnd_typ_mall !=0)){nbend_bnd_typ_mall+= 1;}
if(((ntors_pow_mall % 2)==0)
&&(ntors_pow_mall !=0)){ntors_pow_mall += 1;}
if(((ntors_typ_pow_mall % 2)==0)
&&(ntors_typ_pow_mall !=0)){ntors_typ_pow_mall+= 1;}
if(((ntors_con_mall % 2)==0)
&&(ntors_con_mall !=0)){ntors_pow_mall += 1;}
if(((ntors_typ_con_mall % 2)==0)
&&(ntors_typ_con_mall !=0)){ntors_typ_pow_mall+= 1;}
if(((nonfo_mall % 2)==0)
&&(nonfo_mall !=0)){nonfo_mall += 1;}
if(((nonfo_typ_mall % 2)==0)
&&(nonfo_typ_mall !=0)){nonfo_typ_mall += 1;}
/*======================================================================*/
/* I) Atm stuff: Note constrain flag set here */
/* and charged atoms are counted */
bonded->constrnt.iconstrnt=0;
if(bonded->bond.ncon > 0) bonded->constrnt.iconstrnt=1;
if(bonded->grp_bond_con.num_21 > 0) bonded->constrnt.iconstrnt=1;
if(bonded->grp_bond_con.num_23 > 0) bonded->constrnt.iconstrnt=1;
if(bonded->grp_bond_con.num_33 > 0) bonded->constrnt.iconstrnt=1;
if(bonded->grp_bond_watts.num_33 > 0) bonded->constrnt.iconstrnt=1;
if(bonded->grp_bond_con.num_43 > 0) bonded->constrnt.iconstrnt=1;
if(bonded->grp_bond_con.num_46 > 0) bonded->constrnt.iconstrnt=1;
if(bonded->bend.ncon > 0) bonded->constrnt.iconstrnt=1;
if(bonded->tors.ncon > 0) bonded->constrnt.iconstrnt=1;
clatoms_info->ichrg = (int *)cmalloc(natm_mall*sizeof(int))-1;
clatoms_info->nfree = 0;
clatoms_info->nfree_pimd = 0;
for(i=1;i<=atommaps->nmol_typ;i++){
inow = atommaps->nfree_1mol_jmol_typ[i]
*atommaps->nmol_jmol_typ[i];
know = 3*atommaps->natm_1mol_jmol_typ[i]
*atommaps->nmol_jmol_typ[i];
clatoms_info->nfree += inow;
if(pimd_freez_typ==2){
clatoms_info->nfree_pimd += inow*pi_beads;
}else{
clatoms_info->nfree_pimd += (inow + know*(pi_beads-1));
}/*endif*/
}/*endfor*/
clatoms_info->nchrg = 0;
for(i=1;i<=clatoms_info->natm_tot;i++){
clatoms_info->mass[i] *= PROT_MASS;
if(clatoms_info->q[i] != 0) {
clatoms_info->nchrg++;
clatoms_info->ichrg[(clatoms_info->nchrg)] = i;
}
}
nchrg_mall = clatoms_info->nchrg;
if((nchrg_mall % 2)==0){nchrg_mall += 1;}
now_memory = ((double)(((natm_mall)*sizeof(double)*13+sizeof(int)*4)+
natm_typ_mall*(sizeof(double)*0+sizeof(int)*25))
*1.e-06);
*tot_memory += now_memory;
printf("Atom allocation: %g Mbytes; Total memory: %g Mbytes\n",
now_memory,*tot_memory);
atommaps->atm_typ = (NAME *)crealloc(&(atommaps->atm_typ)[1],
natm_typ_mall*sizeof(NAME))-1;
clatoms_info->mass = (double *)crealloc(&(clatoms_info->mass)[1],
natm_mall*sizeof(double))-1;
clatoms_info->q = (double *)crealloc(&(clatoms_info->q)[1],
natm_mall*sizeof(double))-1;
clatoms_info->cp_vlnc_up = (int *)crealloc(&(clatoms_info->cp_vlnc_up)[1],
natm_mall*sizeof(int))-1;
clatoms_info->cp_vlnc_dn = (int *)crealloc(&(clatoms_info->cp_vlnc_dn)[1],
natm_mall*sizeof(int))-1;
clatoms_info->cp_atm_flag = (int *)crealloc(&(clatoms_info->cp_atm_flag)[1],
natm_mall*sizeof(int))-1;
clatoms_info->ichrg = (int *)crealloc(&(clatoms_info->ichrg)[1],
nchrg_mall*sizeof(int))-1;
clatoms_info->alp_pol = (double *)crealloc(&(clatoms_info->alp_pol)[1],
natm_mall*sizeof(double))-1;
clatoms_info->b_neut = (double *)crealloc(&(clatoms_info->b_neut)[1],
natm_mall*sizeof(double))-1;
clatoms_info->text_atm = (double *)crealloc(&(clatoms_info->text_atm)[1],
natm_mall*sizeof(double))-1;
atommaps->iatm_mol_typ = (int *)crealloc(&(atommaps->iatm_mol_typ)[1],
natm_mall*sizeof(int))-1;
atommaps->iatm_atm_typ = (int *)crealloc(&(atommaps->iatm_atm_typ)[1],
natm_mall*sizeof(int))-1;
atommaps->iatm_res_typ = (int *)crealloc(&(atommaps->iatm_res_typ)[1],
natm_mall*sizeof(int))-1;
atommaps->iatm_mol_num = (int *)crealloc(&(atommaps->iatm_mol_num)[1],
natm_mall*sizeof(int))-1;
atommaps->iatm_res_num = (int *)crealloc(&(atommaps->iatm_res_num)[1],
natm_mall*sizeof(int))-1;
pimd_on = simopts->pimd + simopts->cp_pimd
+ simopts->cp_wave_pimd + simopts->cp_wave_min_pimd
+ simopts->debug_pimd + simopts->debug_cp_pimd;
clatoms_info->xold= (double *)cmalloc(natm_mall*sizeof(double))-1;
clatoms_info->yold= (double *)cmalloc(natm_mall*sizeof(double))-1;
clatoms_info->zold= (double *)cmalloc(natm_mall*sizeof(double))-1;
if(pi_beads>1||pimd_on==1){
clatoms_info->xmod = (double *)cmalloc(natm_mall*sizeof(double))-1;
clatoms_info->ymod = (double *)cmalloc(natm_mall*sizeof(double))-1;
clatoms_info->zmod = (double *)cmalloc(natm_mall*sizeof(double))-1;
}/*endif*/
if(clatoms_info->pi_beads>1||pimd_on==1){
clatoms_info->prekf = (double *)cmalloc(natm_mall*sizeof(double))-1;
}
clatoms_info->roll_sc = (double *)cmalloc(natm_mall*sizeof(double))-1;
/*========================================================================*/
/* I) Ghost_atm stuff */
ghost_atoms->ighost_map = (int *) crealloc(&(ghost_atoms->ighost_map)[1],
nghost_mall*sizeof(int))-1;
ghost_atoms->natm_comp = (int *) crealloc(&(ghost_atoms->natm_comp)[1],
nghost_mall*sizeof(int))-1;
atommaps->ighost_flag = (int *) crealloc(&(atommaps->ighost_flag)[1],
natm_mall*sizeof(int))-1;
/* need to set up reallocate matrix */
ghost_atoms->iatm_comp = creall_int_mat(ghost_atoms->iatm_comp,
1,ncomp_old ,1,nghost_old,
1,ncomp_mall,1,nghost_mall);
ghost_atoms->coef = creall_mat(ghost_atoms->coef,
1,ncomp_old ,1,nghost_old,
1,ncomp_mall,1,nghost_mall);
/*========================================================================*/
/* I) Freeze_atm stuff */
atommaps->freeze_map = (int *) crealloc(&(atommaps->freeze_map)[1],
nfreeze_mall*sizeof(int))-1;
atommaps->freeze_flag = (int *) crealloc(&(atommaps->freeze_flag)[1],
natm_mall*sizeof(int))-1;
atommaps->atom_label = (int *) crealloc(&(atommaps->atom_label)[1],
natm_mall*sizeof(int))-1;
/*========================================================================*/
/* II) Grp constrnts */
bonded->grp_bond_con.j1_21 =
(int *)crealloc(&(bonded->grp_bond_con.j1_21)[1],
ngrp_21_mall*sizeof(int))-1;
bonded->grp_bond_con.j2_21 =
(int *) crealloc(&(bonded->grp_bond_con.j2_21)[1],
ngrp_21_mall*sizeof(int))-1;
bonded->grp_bond_con.jtyp_21 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_21)[1],
ngrp_21_mall*sizeof(int))-1;
bonded->grp_bond_con.j1_33 =
(int *)crealloc(&(bonded->grp_bond_con.j1_33)[1],
ngrp_33_mall*sizeof(int))-1;
bonded->grp_bond_con.j2_33 =
(int *) crealloc(&(bonded->grp_bond_con.j2_33)[1],
ngrp_33_mall*sizeof(int))-1;
bonded->grp_bond_con.j3_33 =
(int *) crealloc(&(bonded->grp_bond_con.j3_33)[1],
ngrp_33_mall*sizeof(int))-1;
bonded->grp_bond_con.jtyp_33 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_33)[1],
ngrp_33_mall*sizeof(int))-1;
bonded->grp_bond_watts.j1_33 =
(int *)crealloc(&(bonded->grp_bond_watts.j1_33)[1],
ngrp_watt_33_mall*sizeof(int))-1;
bonded->grp_bond_watts.j2_33 =
(int *) crealloc(&(bonded->grp_bond_watts.j2_33)[1],
ngrp_watt_33_mall*sizeof(int))-1;
bonded->grp_bond_watts.j3_33 =
(int *) crealloc(&(bonded->grp_bond_watts.j3_33)[1],
ngrp_watt_33_mall*sizeof(int))-1;
bonded->grp_bond_watts.jtyp_33 =
(int *) crealloc(&(bonded->grp_bond_watts.jtyp_33)[1],
ngrp_watt_33_mall*sizeof(int))-1;
bonded->grp_bond_con.j1_23 =
(int *) crealloc(&(bonded->grp_bond_con.j1_23)[1],
ngrp_23_mall*sizeof(int))-1;
bonded->grp_bond_con.j2_23 =
(int *) crealloc(&(bonded->grp_bond_con.j2_23)[1],
ngrp_23_mall*sizeof(int))-1;
bonded->grp_bond_con.j3_23 =
(int *) crealloc(&(bonded->grp_bond_con.j3_23)[1],
ngrp_23_mall*sizeof(int))-1;
bonded->grp_bond_con.jtyp_23 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_23)[1],
ngrp_23_mall*sizeof(int))-1;
bonded->grp_bond_con.j1_43 =
(int *)crealloc(&(bonded->grp_bond_con.j1_43)[1],
ngrp_43_mall*sizeof(int))-1;
bonded->grp_bond_con.j2_43 =
(int *) crealloc(&(bonded->grp_bond_con.j2_43)[1],
ngrp_43_mall*sizeof(int))-1;
bonded->grp_bond_con.j3_43 =
(int *) crealloc(&(bonded->grp_bond_con.j3_43)[1],
ngrp_43_mall*sizeof(int))-1;
bonded->grp_bond_con.j4_43 =
(int *) crealloc(&(bonded->grp_bond_con.j4_43)[1],
ngrp_43_mall*sizeof(int))-1;
bonded->grp_bond_con.jtyp_43 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_43)[1],
ngrp_43_mall*sizeof(int))-1;
bonded->grp_bond_con.j1_46 =
(int *) crealloc(&(bonded->grp_bond_con.j1_46)[1],
ngrp_46_mall*sizeof(int))-1;
bonded->grp_bond_con.j2_46 =
(int *) crealloc(&(bonded->grp_bond_con.j2_46)[1],
ngrp_46_mall*sizeof(int))-1;
bonded->grp_bond_con.j3_46 =
(int *) crealloc(&(bonded->grp_bond_con.j3_46)[1],
ngrp_46_mall*sizeof(int))-1;
bonded->grp_bond_con.j4_46 =
(int *) crealloc(&(bonded->grp_bond_con.j4_46)[1],
ngrp_46_mall*sizeof(int))-1;
bonded->grp_bond_con.jtyp_46 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_46)[1],
ngrp_46_mall*sizeof(int))-1;
bonded->grp_bond_con.al_21 = cmall_mat(1,1,1,ngrp_21_mall);
bonded->grp_bond_con.al_33 = cmall_mat(1,3,1,ngrp_33_mall);
bonded->grp_bond_con.al_43 = cmall_mat(1,3,1,ngrp_43_mall);
bonded->grp_bond_con.al_23 = cmall_mat(1,2,1,ngrp_23_mall);
bonded->grp_bond_con.al_46 = cmall_mat(1,6,1,ngrp_46_mall);
bonded->grp_bond_con.eq_21 = cmall_mat(1,1,1,ngrp_typ_21_mall);
bonded->grp_bond_con.eq_33 = cmall_mat(1,3,1,ngrp_typ_33_mall);
bonded->grp_bond_watts.eq_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_con.eq_43 = cmall_mat(1,3,1,ngrp_typ_43_mall);
bonded->grp_bond_con.eq_23 = cmall_mat(1,2,1,ngrp_typ_23_mall);
bonded->grp_bond_con.eq_46 = cmall_mat(1,6,1,ngrp_typ_46_mall);
bonded->grp_bond_watts.cos_thet0_2 =
(double *)malloc(ngrp_typ_watt_33_mall*sizeof(int))-1;
bonded->grp_bond_watts.sin_thet0_2 =
(double *)malloc(ngrp_typ_watt_33_mall*sizeof(int))-1;
bonded->grp_bond_watts.c_0_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.c_1_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.c_2_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.c_3_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.c_4_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.c_5_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.c_6_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.dc_0_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.dc_1_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.dc_2_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.dc_3_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.dc_4_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.dc_5_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.dc_6_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
/*======================================================================*/
/* II) Bonds */
now_memory = ((nbond_pow_mall)*(sizeof(double)*0+sizeof(int)*3)+
(nbond_con_mall)*(sizeof(double)*1 + sizeof(int)*3)+
(nbond_typ_pow_mall)*(sizeof(double)*14+ sizeof(int)*0 )+
(nbond_typ_con_mall)*(sizeof(double)*1 + sizeof(int)*0)+
(nbend_pow_mall)*(sizeof(double)*0 + sizeof(int)*4)+
(nbend_typ_pow_mall)*(sizeof(double)*29+ sizeof(int)*0)+
(nbend_con_mall)*(sizeof(double)*1 + sizeof(int)*4)+
(nbend_typ_con_mall)*(sizeof(double)*1 + sizeof(int)*0)+
(nbend_bnd_mall)*(sizeof(double)*0 + sizeof(int)*4)+
(nbend_bnd_typ_mall)*(sizeof(double)*44 + sizeof(int)*0)+
(ntors_pow_mall)*(sizeof(double)*0 + sizeof(int)*5)+
(ntors_con_mall)*(sizeof(double)*1 + sizeof(int)*5)+
(ntors_typ_pow_mall)*(sizeof(double)*30 + sizeof(int)*0)+
(nonfo_mall)*(sizeof(double)*0 + sizeof(int)*3)+
(nonfo_typ_mall)*(sizeof(double)*3 + sizeof(int)*0)
)*1.e-06;
*tot_memory += now_memory;
printf("Intramolecular allocation: %g Mbytes; Total memory: %g Mbytes\n",
now_memory,*tot_memory);
ntyp_pow = nbond_typ_pow_mall;
bonded->bond.j1_pow = (int *) crealloc(&(bonded->bond.j1_pow)[1],
nbond_pow_mall*sizeof(int))-1;
bonded->bond.j2_pow = (int *) crealloc(&(bonded->bond.j2_pow)[1],
nbond_pow_mall*sizeof(int))-1;
bonded->bond.jtyp_pow = (int *)crealloc(&(bonded->bond.jtyp_pow)[1],
nbond_pow_mall*sizeof(int))-1;
bonded->bond.j1_con = (int *) crealloc(&(bonded->bond.j1_con)[1],
nbond_con_mall*sizeof(int))-1;
bonded->bond.j2_con = (int *) crealloc(&(bonded->bond.j2_con)[1],
nbond_con_mall*sizeof(int))-1;
bonded->bond.jtyp_con = (int *)crealloc(&(bonded->bond.jtyp_con)[1],
nbond_con_mall*sizeof(int))-1;
bonded->bond.al_con = (double *)cmalloc(nbond_con_mall*sizeof(double))-1;
bonded->bond.eq_pow = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.eq_pow_res = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.c_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.c_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.c_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.c_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.c_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.c_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.c_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.dc_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.dc_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.dc_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.dc_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.dc_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.dc_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.dc_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.eq_con = (double *)cmalloc(nbond_typ_con_mall
*sizeof(double))-1;
null_inter_parse->jbond1_nul= (int *)
crealloc(&(null_inter_parse->jbond1_nul)[1],
null_inter_parse->nbond_nul*sizeof(int))-1;
null_inter_parse->jbond2_nul= (int *)
crealloc(&(null_inter_parse->jbond2_nul)[1],
null_inter_parse->nbond_nul*sizeof(int))-1;
/*=======================================================================*/
/* III) Bends */
ntyp_pow = nbend_typ_pow_mall;
bonded->bend.j1_pow = (int *) crealloc(&(bonded->bend.j1_pow)[1],
nbend_pow_mall*sizeof(int))-1;
bonded->bend.j2_pow = (int *) crealloc(&(bonded->bend.j2_pow)[1],
nbend_pow_mall*sizeof(int))-1;
bonded->bend.j3_pow = (int *) crealloc(&(bonded->bend.j3_pow)[1],
nbend_pow_mall*sizeof(int))-1;
bonded->bend.jtyp_pow = (int *)crealloc(&(bonded->bend.jtyp_pow)[1],
nbend_pow_mall*sizeof(int))-1;
bonded->bend.j1_con = (int *) crealloc(&(bonded->bend.j1_con)[1],
nbend_con_mall*sizeof(int))-1;
bonded->bend.j2_con = (int *) crealloc(&(bonded->bend.j2_con)[1],
nbend_con_mall*sizeof(int))-1;
bonded->bend.j3_con = (int *) crealloc(&(bonded->bend.j3_con)[1],
nbend_con_mall*sizeof(int))-1;
bonded->bend.jtyp_con = (int *)crealloc(&(bonded->bend.jtyp_con)[1],
nbend_con_mall*sizeof(int))-1;
bonded->bend.eq_pow = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.c_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.c_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.c_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.c_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.c_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.c_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.c_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.s_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.s_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.s_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.s_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.s_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.s_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.s_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.dc_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.dc_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.dc_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.dc_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.dc_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.dc_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.dc_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.ds_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.ds_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.ds_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.ds_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.ds_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.ds_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.ds_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.eq_con = (double *)cmalloc(nbend_typ_con_mall
*sizeof(double))-1;
bonded->bend.al_con = (double *)cmalloc(nbend_con_mall
*sizeof(double))-1;
null_inter_parse->jbend1_nul= (int *)
crealloc(&(null_inter_parse->jbend1_nul)[1],
null_inter_parse->nbend_nul*sizeof(int))-1;
null_inter_parse->jbend2_nul= (int *)
crealloc(&(null_inter_parse->jbend2_nul)[1],
null_inter_parse->nbend_nul*sizeof(int))-1;
null_inter_parse->jbend3_nul= (int *)
crealloc(&(null_inter_parse->jbend3_nul)[1],
null_inter_parse->nbend_nul*sizeof(int))-1;
/*=======================================================================*/
/* III) Bend_bnds */
bonded->bend_bnd.j1 = (int *) crealloc(&(bonded->bend_bnd.j1)[1],
nbend_bnd_mall*sizeof(int))-1;
bonded->bend_bnd.j2 = (int *) crealloc(&(bonded->bend_bnd.j2)[1],
nbend_bnd_mall*sizeof(int))-1;
bonded->bend_bnd.j3 = (int *) crealloc(&(bonded->bend_bnd.j3)[1],
nbend_bnd_mall*sizeof(int))-1;
bonded->bend_bnd.jtyp = (int *)crealloc(&(bonded->bend_bnd.jtyp)[1],
nbend_bnd_mall*sizeof(int))-1;
bonded->bend_bnd.eq_bond = (double *)cmalloc(nbend_bnd_typ_mall*
sizeof(double))-1;
bonded->bend_bnd.eq_bend = (double *)cmalloc(nbend_bnd_typ_mall*
sizeof(double))-1;
bonded->bend_bnd.cbond_0 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbond_1 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbond_2 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbond_3 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbond_4 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbond_5 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbond_6 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbond_0 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbond_1 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbond_2 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbond_3 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbond_4 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbond_5 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbond_6 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbend_0 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbend_1 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbend_2 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbend_3 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbend_4 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbend_5 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbend_6 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.sbend_0 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.sbend_1 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.sbend_2 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.sbend_3 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.sbend_4 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.sbend_5 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.sbend_6 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbend_0 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbend_1 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbend_2 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbend_3 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbend_4 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbend_5 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbend_6 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dsbend_0 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dsbend_1 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dsbend_2 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dsbend_3 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dsbend_4 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dsbend_5 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dsbend_6 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
/*======================================================================*/
/* IV) Tors */
ntyp_pow = ntors_typ_pow_mall;
bonded->tors.j1_pow = (int *) crealloc(&(bonded->tors.j1_pow)[1],
ntors_pow_mall*sizeof(int))-1;
bonded->tors.j2_pow = (int *) crealloc(&(bonded->tors.j2_pow)[1],
ntors_pow_mall*sizeof(int))-1;
bonded->tors.j3_pow = (int *) crealloc(&(bonded->tors.j3_pow)[1],
ntors_pow_mall*sizeof(int))-1;
bonded->tors.j4_pow = (int *) crealloc(&(bonded->tors.j4_pow)[1],
ntors_pow_mall*sizeof(int))-1;
bonded->tors.jtyp_pow = (int *)crealloc(&(bonded->tors.jtyp_pow)[1],
ntors_pow_mall*sizeof(int))-1;
bonded->tors.j1_con = (int *) crealloc(&(bonded->tors.j1_con)[1],
ntors_con_mall*sizeof(int))-1;
bonded->tors.j2_con = (int *) crealloc(&(bonded->tors.j2_con)[1],
ntors_con_mall*sizeof(int))-1;
bonded->tors.j3_con = (int *) crealloc(&(bonded->tors.j3_con)[1],
ntors_con_mall*sizeof(int))-1;
bonded->tors.j4_con = (int *) crealloc(&(bonded->tors.j4_con)[1],
ntors_con_mall*sizeof(int))-1;
bonded->tors.jtyp_con = (int *)crealloc(&(bonded->tors.jtyp_con)[1],
ntors_con_mall*sizeof(int))-1;
bonded->tors.al_con = (double *)cmalloc(ntors_con_mall
*sizeof(double))-1;
bonded->tors.eq_pow = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.c_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.c_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.c_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.c_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.c_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.c_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.c_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.s_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.s_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.s_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.s_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.s_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.s_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.s_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.dc_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.dc_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.dc_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.dc_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.dc_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.dc_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.dc_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.ds_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.ds_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.ds_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.ds_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.ds_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.ds_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.ds_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.eq_con = (double *)cmalloc(ntors_typ_pow_mall
*sizeof(double))-1;
null_inter_parse->jtors1_nul= (int *)
crealloc(&(null_inter_parse->jtors1_nul)[1],
null_inter_parse->ntors_nul*sizeof(int))-1;
null_inter_parse->jtors2_nul= (int *)
crealloc(&(null_inter_parse->jtors2_nul)[1],
null_inter_parse->ntors_nul*sizeof(int))-1;
null_inter_parse->jtors3_nul= (int *)
crealloc(&(null_inter_parse->jtors3_nul)[1],
null_inter_parse->ntors_nul*sizeof(int))-1;
null_inter_parse->jtors4_nul= (int *)
crealloc(&(null_inter_parse->jtors4_nul)[1],
null_inter_parse->ntors_nul*sizeof(int))-1;
/*=======================================================================*/
/* V) Onfo */
bonded->onfo.j1 = (int *) crealloc(&(bonded->onfo.j1)[1],
nonfo_mall*sizeof(int))-1;
bonded->onfo.j2 = (int *) crealloc(&(bonded->onfo.j2)[1],
nonfo_mall*sizeof(int))-1;
bonded->onfo.jtyp = (int *) crealloc(&(bonded->onfo.jtyp)[1],
nonfo_mall*sizeof(int))-1;
bonded->onfo.feps = (double *)cmalloc(nonfo_typ_mall*sizeof(double))-1;
bonded->onfo.s6 = (double *)cmalloc(nonfo_typ_mall*sizeof(double))-1;
bonded->onfo.sc = (double *)cmalloc(nonfo_typ_mall*sizeof(double))-1;
null_inter_parse->jonfo1_nul= (int *)
crealloc(&(null_inter_parse->jonfo1_nul)[1],
null_inter_parse->nonfo_nul*sizeof(int))-1;
null_inter_parse->jonfo2_nul = (int *)
crealloc(&(null_inter_parse->jonfo2_nul)[1],
null_inter_parse->nonfo_nul*sizeof(int))-1;
/*=======================================================================*/
/* V) Assign mall variables */
clatoms_info->natm_mall = natm_mall;
clatoms_info->nchrg_mall = nchrg_mall;
ghost_atoms->nghost_mall = nghost_mall;
ghost_atoms->ncomp_mall = ncomp_mall;
atommaps->nfreeze_mall = nfreeze_mall;
atommaps->natm_typ_mall = natm_typ_mall;
bonded->bond.nbond_pow_mall = nbond_pow_mall;
bonded->bond.nbond_typ_pow_mall = nbond_typ_pow_mall;
bonded->bond.nbond_con_mall = nbond_con_mall;
bonded->bond.nbond_typ_con_mall = nbond_typ_con_mall;
bonded->grp_bond_con.ngrp_21_mall = ngrp_21_mall;
bonded->grp_bond_watts.ngrp_33_mall = ngrp_watt_33_mall;
bonded->grp_bond_con.ngrp_33_mall = ngrp_33_mall;
bonded->grp_bond_con.ngrp_43_mall = ngrp_43_mall;
bonded->grp_bond_con.ngrp_23_mall = ngrp_23_mall;
bonded->grp_bond_con.ngrp_46_mall = ngrp_46_mall;
bonded->grp_bond_con.ngrp_typ_21_mall = ngrp_typ_21_mall;
bonded->grp_bond_con.ngrp_typ_33_mall = ngrp_typ_33_mall;
bonded->grp_bond_watts.ngrp_typ_33_mall = ngrp_typ_watt_33_mall;
bonded->grp_bond_con.ngrp_typ_43_mall = ngrp_typ_43_mall;
bonded->grp_bond_con.ngrp_typ_23_mall = ngrp_typ_23_mall;
bonded->grp_bond_con.ngrp_typ_46_mall = ngrp_typ_46_mall;
bonded->bend.nbend_con_mall = nbend_con_mall;
bonded->bend.nbend_typ_con_mall = nbend_typ_con_mall;
bonded->bend.nbend_pow_mall = nbend_pow_mall;
bonded->bend.nbend_typ_pow_mall = nbend_typ_pow_mall;
bonded->bend_bnd.nbend_bnd_mall = nbend_bnd_mall;
bonded->bend_bnd.nbend_bnd_typ_mall = nbend_bnd_typ_mall;
bonded->tors.ntors_pow_mall = ntors_pow_mall;
bonded->tors.ntors_typ_pow_mall = ntors_typ_pow_mall;
bonded->tors.ntors_con_mall = ntors_con_mall;
bonded->tors.ntors_typ_con_mall = ntors_typ_con_mall;
bonded->onfo.nonfo_mall = nonfo_mall;
bonded->onfo.nonfo_typ_mall = nonfo_typ_mall;
/*-----------------------------------------------------------------------*/
}/*end routine*/
