Loading host/inc/stringify.h +197 −12 Original line number Diff line number Diff line Loading @@ -3,14 +3,29 @@ #define STRINGIFY_H const char *calcenergy_ocl = "/*\n" " * (C) 2013. Evopro Innovation Kft.\n" " *\n" " * defines.h\n" " *\n" " * Created on: 2009.05.29.\n" " * Author: pechan.imre\n" "\n" "OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm\n" "Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.\n" "\n" "AutoDock is a Trade Mark of the Scripps Research Institute.\n" "\n" "This program is free software; you can redistribute it and/or\n" "modify it under the terms of the GNU General Public License\n" "as published by the Free Software Foundation; either version 2\n" "of the License, or (at your option) any later version.\n" "\n" "This program is distributed in the hope that it will be useful,\n" "but WITHOUT ANY WARRANTY; without even the implied warranty of\n" "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" "GNU General Public License for more details.\n" "\n" "You should have received a copy of the GNU General Public License\n" "along with this program; if not, write to the Free Software\n" "Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n" "\n" "*/\n" "\n" "\n" "#ifndef DEFINES_H_\n" "#define DEFINES_H_\n" "\n" Loading @@ -22,15 +37,17 @@ const char *calcenergy_ocl = " #define NUM_OF_THREADS_PER_BLOCK 64\n" "#elif defined (N128WI)\n" " #define NUM_OF_THREADS_PER_BLOCK 128\n" "#elif defined (N256WI)\n" " #define NUM_OF_THREADS_PER_BLOCK 256\n" "#else\n" " #define NUM_OF_THREADS_PER_BLOCK 64\n" "#endif\n" "\n" "#define MAX_NUM_OF_ATOMS 90\n" "#define MAX_NUM_OF_ATOMS 256\n" "#define MAX_NUM_OF_ATYPES 14\n" "#define MAX_INTRAE_CONTRIBUTORS 8128\n" "#define MAX_NUM_OF_ROTATIONS 4096\n" "#define MAX_NUM_OF_ROTBONDS 32\n" "#define MAX_INTRAE_CONTRIBUTORS MAX_NUM_OF_ATOMS * MAX_NUM_OF_ATOMS\n" "#define MAX_NUM_OF_ROTATIONS MAX_NUM_OF_ATOMS * MAX_NUM_OF_ROTBONDS\n" "#define MAX_POPSIZE 2048\n" "#define MAX_NUM_OF_RUNS 1000\n" "\n" Loading @@ -49,6 +66,30 @@ const char *calcenergy_ocl = "#define MAPPED_COPY\n" "\n" "#endif /* DEFINES_H_ */\n" "/*\n" "\n" "OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm\n" "Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.\n" "\n" "AutoDock is a Trade Mark of the Scripps Research Institute.\n" "\n" "This program is free software; you can redistribute it and/or\n" "modify it under the terms of the GNU General Public License\n" "as published by the Free Software Foundation; either version 2\n" "of the License, or (at your option) any later version.\n" "\n" "This program is distributed in the hope that it will be useful,\n" "but WITHOUT ANY WARRANTY; without even the implied warranty of\n" "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" "GNU General Public License for more details.\n" "\n" "You should have received a copy of the GNU General Public License\n" "along with this program; if not, write to the Free Software\n" "Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n" "\n" "*/\n" "\n" "\n" "#ifndef CALCENERGY_BASIC_H_\n" "#define CALCENERGY_BASIC_H_\n" "\n" Loading Loading @@ -84,6 +125,30 @@ const char *calcenergy_ocl = " cube[0][1][1]*weights[0][1][1] +cube[1][1][1]*weights[1][1][1])\n" "\n" "#endif /* CALCENERGY_BASIC_H_ */\n" "/*\n" "\n" "OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm\n" "Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.\n" "\n" "AutoDock is a Trade Mark of the Scripps Research Institute.\n" "\n" "This program is free software; you can redistribute it and/or\n" "modify it under the terms of the GNU General Public License\n" "as published by the Free Software Foundation; either version 2\n" "of the License, or (at your option) any later version.\n" "\n" "This program is distributed in the hope that it will be useful,\n" "but WITHOUT ANY WARRANTY; without even the implied warranty of\n" "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" "GNU General Public License for more details.\n" "\n" "You should have received a copy of the GNU General Public License\n" "along with this program; if not, write to the Free Software\n" "Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n" "\n" "*/\n" "\n" "\n" "\n" "// All related pragmas are in defines.h (accesible by host and device code)\n" "\n" Loading Loading @@ -137,7 +202,7 @@ const char *calcenergy_ocl = "//determines which reference orientation should be used.\n" "{\n" " int contributor_counter;\n" " char atom1_id, atom2_id, atom1_typeid, atom2_typeid;\n" " /*char*/uint atom1_id, atom2_id, atom1_typeid, atom2_typeid;\n" "\n" " // Name changed to distance_leo to avoid\n" " // errors as \"distance\" is the name of OpenCL function\n" Loading Loading @@ -677,6 +742,30 @@ const char *calcenergy_ocl = " }\n" "}\n" "\n" "/*\n" "\n" "OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm\n" "Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.\n" "\n" "AutoDock is a Trade Mark of the Scripps Research Institute.\n" "\n" "This program is free software; you can redistribute it and/or\n" "modify it under the terms of the GNU General Public License\n" "as published by the Free Software Foundation; either version 2\n" "of the License, or (at your option) any later version.\n" "\n" "This program is distributed in the hope that it will be useful,\n" "but WITHOUT ANY WARRANTY; without even the implied warranty of\n" "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" "GNU General Public License for more details.\n" "\n" "You should have received a copy of the GNU General Public License\n" "along with this program; if not, write to the Free Software\n" "Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n" "\n" "*/\n" "\n" "\n" "__kernel void __attribute__ ((reqd_work_group_size(NUM_OF_THREADS_PER_BLOCK,1,1)))\n" "gpu_calc_initpop( char dockpars_num_of_atoms,\n" " char dockpars_num_of_atypes,\n" Loading Loading @@ -788,6 +877,30 @@ const char *calcenergy_ocl = " dockpars_evals_of_new_entities[get_group_id(0)] = 1;\n" " }\n" "}\n" "/*\n" "\n" "OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm\n" "Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.\n" "\n" "AutoDock is a Trade Mark of the Scripps Research Institute.\n" "\n" "This program is free software; you can redistribute it and/or\n" "modify it under the terms of the GNU General Public License\n" "as published by the Free Software Foundation; either version 2\n" "of the License, or (at your option) any later version.\n" "\n" "This program is distributed in the hope that it will be useful,\n" "but WITHOUT ANY WARRANTY; without even the implied warranty of\n" "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" "GNU General Public License for more details.\n" "\n" "You should have received a copy of the GNU General Public License\n" "along with this program; if not, write to the Free Software\n" "Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n" "\n" "*/\n" "\n" "\n" "__kernel void __attribute__ ((reqd_work_group_size(NUM_OF_THREADS_PER_BLOCK,1,1)))\n" "gpu_sum_evals(/*unsigned long pop_size,*/\n" " unsigned int pop_size,\n" Loading Loading @@ -844,6 +957,30 @@ const char *calcenergy_ocl = " evals_of_runs[get_group_id(0)] += sum_evals;\n" " }\n" "}\n" "/*\n" "\n" "OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm\n" "Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.\n" "\n" "AutoDock is a Trade Mark of the Scripps Research Institute.\n" "\n" "This program is free software; you can redistribute it and/or\n" "modify it under the terms of the GNU General Public License\n" "as published by the Free Software Foundation; either version 2\n" "of the License, or (at your option) any later version.\n" "\n" "This program is distributed in the hope that it will be useful,\n" "but WITHOUT ANY WARRANTY; without even the implied warranty of\n" "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" "GNU General Public License for more details.\n" "\n" "You should have received a copy of the GNU General Public License\n" "along with this program; if not, write to the Free Software\n" "Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n" "\n" "*/\n" "\n" "\n" "// -------------------------------------------------------\n" "//\n" "// -------------------------------------------------------\n" Loading Loading @@ -1032,6 +1169,30 @@ const char *calcenergy_ocl = " //dockpars_conformations_next[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+gene_counter] = dockpars_conformations_current[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+GENOTYPE_LENGTH_IN_GLOBMEM*best_ID+gene_counter];\n" " dockpars_conformations_next[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+gene_counter] = dockpars_conformations_current[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+GENOTYPE_LENGTH_IN_GLOBMEM*best_ID[0]+gene_counter];\n" "}\n" "/*\n" "\n" "OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm\n" "Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.\n" "\n" "AutoDock is a Trade Mark of the Scripps Research Institute.\n" "\n" "This program is free software; you can redistribute it and/or\n" "modify it under the terms of the GNU General Public License\n" "as published by the Free Software Foundation; either version 2\n" "of the License, or (at your option) any later version.\n" "\n" "This program is distributed in the hope that it will be useful,\n" "but WITHOUT ANY WARRANTY; without even the implied warranty of\n" "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" "GNU General Public License for more details.\n" "\n" "You should have received a copy of the GNU General Public License\n" "along with this program; if not, write to the Free Software\n" "Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n" "\n" "*/\n" "\n" "\n" "__kernel void __attribute__ ((reqd_work_group_size(NUM_OF_THREADS_PER_BLOCK,1,1)))\n" "perform_LS( char dockpars_num_of_atoms,\n" " char dockpars_num_of_atypes,\n" Loading Loading @@ -1400,6 +1561,30 @@ const char *calcenergy_ocl = " dockpars_conformations_next[(run_id*dockpars_pop_size+entity_id)*GENOTYPE_LENGTH_IN_GLOBMEM+gene_counter] = offspring_genotype[gene_counter];\n" "#endif\n" "}\n" "/*\n" "\n" "OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm\n" "Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.\n" "\n" "AutoDock is a Trade Mark of the Scripps Research Institute.\n" "\n" "This program is free software; you can redistribute it and/or\n" "modify it under the terms of the GNU General Public License\n" "as published by the Free Software Foundation; either version 2\n" "of the License, or (at your option) any later version.\n" "\n" "This program is distributed in the hope that it will be useful,\n" "but WITHOUT ANY WARRANTY; without even the implied warranty of\n" "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" "GNU General Public License for more details.\n" "\n" "You should have received a copy of the GNU General Public License\n" "along with this program; if not, write to the Free Software\n" "Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n" "\n" "*/\n" "\n" "\n" "__kernel void __attribute__ ((reqd_work_group_size(NUM_OF_THREADS_PER_BLOCK,1,1)))\n" "gpu_gen_and_eval_newpops(char dockpars_num_of_atoms,\n" " char dockpars_num_of_atypes,\n" Loading host/src/processligand.cpp +4 −3 Original line number Diff line number Diff line Loading @@ -755,13 +755,14 @@ int get_liganddata(const char* ligfilename, Liganddata* myligand, const double A myligand->atom_rigid_structures [atom_counter] = current_rigid_struct_id; //using the id of the current rigid structure atom_counter++; #if 0 // include last atom if (atom_counter == myligand->num_of_atoms) { for (i=0; i<branch_counter; i++) //for all branches found until now if (branches [i][2] == 1) //if it is open, the atom has to be rotated atom_rotbonds_temp [atom_counter][i] = 1; //modifying atom_rotbonds_temp } #endif } if (strcmp(tempstr, "BRANCH") == 0) //if new branch, stroing atom indexes into branches [][] Loading Loading @@ -792,7 +793,7 @@ int get_liganddata(const char* ligfilename, Liganddata* myligand, const double A fscanf(fp, "%d", &(myligand->rotbonds [endbranch_counter][1])); //of endbranches (myligand->rotbonds [endbranch_counter][0])--; (myligand->rotbonds [endbranch_counter][1])--; #if 0 // include last atom before ENDBRANCH //if (atom_counter == myligand->num_of_atoms) { for (i=0; i<branch_counter; i++) //for all branches found until now Loading @@ -812,7 +813,7 @@ int get_liganddata(const char* ligfilename, Liganddata* myligand, const double A } */ // --------------------------- #endif for (i=0; i<branch_counter; i++) //the branch have to be closed if ((branches [i][0] == myligand->rotbonds [endbranch_counter][0]) && (branches [i][1] == myligand->rotbonds [endbranch_counter][1])) Loading prebuilt/linux/ocladock_cpu_128wi +264 B (191 KiB) File changed.No diff preview for this file type. View original file View changed file prebuilt/linux/ocladock_cpu_16wi +264 B (191 KiB) File changed.No diff preview for this file type. View original file View changed file prebuilt/linux/ocladock_cpu_256wi +264 B (191 KiB) File changed.No diff preview for this file type. View original file View changed file Loading
host/inc/stringify.h +197 −12 Original line number Diff line number Diff line Loading @@ -3,14 +3,29 @@ #define STRINGIFY_H const char *calcenergy_ocl = "/*\n" " * (C) 2013. Evopro Innovation Kft.\n" " *\n" " * defines.h\n" " *\n" " * Created on: 2009.05.29.\n" " * Author: pechan.imre\n" "\n" "OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm\n" "Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.\n" "\n" "AutoDock is a Trade Mark of the Scripps Research Institute.\n" "\n" "This program is free software; you can redistribute it and/or\n" "modify it under the terms of the GNU General Public License\n" "as published by the Free Software Foundation; either version 2\n" "of the License, or (at your option) any later version.\n" "\n" "This program is distributed in the hope that it will be useful,\n" "but WITHOUT ANY WARRANTY; without even the implied warranty of\n" "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" "GNU General Public License for more details.\n" "\n" "You should have received a copy of the GNU General Public License\n" "along with this program; if not, write to the Free Software\n" "Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n" "\n" "*/\n" "\n" "\n" "#ifndef DEFINES_H_\n" "#define DEFINES_H_\n" "\n" Loading @@ -22,15 +37,17 @@ const char *calcenergy_ocl = " #define NUM_OF_THREADS_PER_BLOCK 64\n" "#elif defined (N128WI)\n" " #define NUM_OF_THREADS_PER_BLOCK 128\n" "#elif defined (N256WI)\n" " #define NUM_OF_THREADS_PER_BLOCK 256\n" "#else\n" " #define NUM_OF_THREADS_PER_BLOCK 64\n" "#endif\n" "\n" "#define MAX_NUM_OF_ATOMS 90\n" "#define MAX_NUM_OF_ATOMS 256\n" "#define MAX_NUM_OF_ATYPES 14\n" "#define MAX_INTRAE_CONTRIBUTORS 8128\n" "#define MAX_NUM_OF_ROTATIONS 4096\n" "#define MAX_NUM_OF_ROTBONDS 32\n" "#define MAX_INTRAE_CONTRIBUTORS MAX_NUM_OF_ATOMS * MAX_NUM_OF_ATOMS\n" "#define MAX_NUM_OF_ROTATIONS MAX_NUM_OF_ATOMS * MAX_NUM_OF_ROTBONDS\n" "#define MAX_POPSIZE 2048\n" "#define MAX_NUM_OF_RUNS 1000\n" "\n" Loading @@ -49,6 +66,30 @@ const char *calcenergy_ocl = "#define MAPPED_COPY\n" "\n" "#endif /* DEFINES_H_ */\n" "/*\n" "\n" "OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm\n" "Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.\n" "\n" "AutoDock is a Trade Mark of the Scripps Research Institute.\n" "\n" "This program is free software; you can redistribute it and/or\n" "modify it under the terms of the GNU General Public License\n" "as published by the Free Software Foundation; either version 2\n" "of the License, or (at your option) any later version.\n" "\n" "This program is distributed in the hope that it will be useful,\n" "but WITHOUT ANY WARRANTY; without even the implied warranty of\n" "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" "GNU General Public License for more details.\n" "\n" "You should have received a copy of the GNU General Public License\n" "along with this program; if not, write to the Free Software\n" "Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n" "\n" "*/\n" "\n" "\n" "#ifndef CALCENERGY_BASIC_H_\n" "#define CALCENERGY_BASIC_H_\n" "\n" Loading Loading @@ -84,6 +125,30 @@ const char *calcenergy_ocl = " cube[0][1][1]*weights[0][1][1] +cube[1][1][1]*weights[1][1][1])\n" "\n" "#endif /* CALCENERGY_BASIC_H_ */\n" "/*\n" "\n" "OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm\n" "Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.\n" "\n" "AutoDock is a Trade Mark of the Scripps Research Institute.\n" "\n" "This program is free software; you can redistribute it and/or\n" "modify it under the terms of the GNU General Public License\n" "as published by the Free Software Foundation; either version 2\n" "of the License, or (at your option) any later version.\n" "\n" "This program is distributed in the hope that it will be useful,\n" "but WITHOUT ANY WARRANTY; without even the implied warranty of\n" "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" "GNU General Public License for more details.\n" "\n" "You should have received a copy of the GNU General Public License\n" "along with this program; if not, write to the Free Software\n" "Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n" "\n" "*/\n" "\n" "\n" "\n" "// All related pragmas are in defines.h (accesible by host and device code)\n" "\n" Loading Loading @@ -137,7 +202,7 @@ const char *calcenergy_ocl = "//determines which reference orientation should be used.\n" "{\n" " int contributor_counter;\n" " char atom1_id, atom2_id, atom1_typeid, atom2_typeid;\n" " /*char*/uint atom1_id, atom2_id, atom1_typeid, atom2_typeid;\n" "\n" " // Name changed to distance_leo to avoid\n" " // errors as \"distance\" is the name of OpenCL function\n" Loading Loading @@ -677,6 +742,30 @@ const char *calcenergy_ocl = " }\n" "}\n" "\n" "/*\n" "\n" "OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm\n" "Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.\n" "\n" "AutoDock is a Trade Mark of the Scripps Research Institute.\n" "\n" "This program is free software; you can redistribute it and/or\n" "modify it under the terms of the GNU General Public License\n" "as published by the Free Software Foundation; either version 2\n" "of the License, or (at your option) any later version.\n" "\n" "This program is distributed in the hope that it will be useful,\n" "but WITHOUT ANY WARRANTY; without even the implied warranty of\n" "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" "GNU General Public License for more details.\n" "\n" "You should have received a copy of the GNU General Public License\n" "along with this program; if not, write to the Free Software\n" "Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n" "\n" "*/\n" "\n" "\n" "__kernel void __attribute__ ((reqd_work_group_size(NUM_OF_THREADS_PER_BLOCK,1,1)))\n" "gpu_calc_initpop( char dockpars_num_of_atoms,\n" " char dockpars_num_of_atypes,\n" Loading Loading @@ -788,6 +877,30 @@ const char *calcenergy_ocl = " dockpars_evals_of_new_entities[get_group_id(0)] = 1;\n" " }\n" "}\n" "/*\n" "\n" "OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm\n" "Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.\n" "\n" "AutoDock is a Trade Mark of the Scripps Research Institute.\n" "\n" "This program is free software; you can redistribute it and/or\n" "modify it under the terms of the GNU General Public License\n" "as published by the Free Software Foundation; either version 2\n" "of the License, or (at your option) any later version.\n" "\n" "This program is distributed in the hope that it will be useful,\n" "but WITHOUT ANY WARRANTY; without even the implied warranty of\n" "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" "GNU General Public License for more details.\n" "\n" "You should have received a copy of the GNU General Public License\n" "along with this program; if not, write to the Free Software\n" "Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n" "\n" "*/\n" "\n" "\n" "__kernel void __attribute__ ((reqd_work_group_size(NUM_OF_THREADS_PER_BLOCK,1,1)))\n" "gpu_sum_evals(/*unsigned long pop_size,*/\n" " unsigned int pop_size,\n" Loading Loading @@ -844,6 +957,30 @@ const char *calcenergy_ocl = " evals_of_runs[get_group_id(0)] += sum_evals;\n" " }\n" "}\n" "/*\n" "\n" "OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm\n" "Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.\n" "\n" "AutoDock is a Trade Mark of the Scripps Research Institute.\n" "\n" "This program is free software; you can redistribute it and/or\n" "modify it under the terms of the GNU General Public License\n" "as published by the Free Software Foundation; either version 2\n" "of the License, or (at your option) any later version.\n" "\n" "This program is distributed in the hope that it will be useful,\n" "but WITHOUT ANY WARRANTY; without even the implied warranty of\n" "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" "GNU General Public License for more details.\n" "\n" "You should have received a copy of the GNU General Public License\n" "along with this program; if not, write to the Free Software\n" "Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n" "\n" "*/\n" "\n" "\n" "// -------------------------------------------------------\n" "//\n" "// -------------------------------------------------------\n" Loading Loading @@ -1032,6 +1169,30 @@ const char *calcenergy_ocl = " //dockpars_conformations_next[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+gene_counter] = dockpars_conformations_current[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+GENOTYPE_LENGTH_IN_GLOBMEM*best_ID+gene_counter];\n" " dockpars_conformations_next[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+gene_counter] = dockpars_conformations_current[GENOTYPE_LENGTH_IN_GLOBMEM*get_group_id(0)+GENOTYPE_LENGTH_IN_GLOBMEM*best_ID[0]+gene_counter];\n" "}\n" "/*\n" "\n" "OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm\n" "Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.\n" "\n" "AutoDock is a Trade Mark of the Scripps Research Institute.\n" "\n" "This program is free software; you can redistribute it and/or\n" "modify it under the terms of the GNU General Public License\n" "as published by the Free Software Foundation; either version 2\n" "of the License, or (at your option) any later version.\n" "\n" "This program is distributed in the hope that it will be useful,\n" "but WITHOUT ANY WARRANTY; without even the implied warranty of\n" "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" "GNU General Public License for more details.\n" "\n" "You should have received a copy of the GNU General Public License\n" "along with this program; if not, write to the Free Software\n" "Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n" "\n" "*/\n" "\n" "\n" "__kernel void __attribute__ ((reqd_work_group_size(NUM_OF_THREADS_PER_BLOCK,1,1)))\n" "perform_LS( char dockpars_num_of_atoms,\n" " char dockpars_num_of_atypes,\n" Loading Loading @@ -1400,6 +1561,30 @@ const char *calcenergy_ocl = " dockpars_conformations_next[(run_id*dockpars_pop_size+entity_id)*GENOTYPE_LENGTH_IN_GLOBMEM+gene_counter] = offspring_genotype[gene_counter];\n" "#endif\n" "}\n" "/*\n" "\n" "OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm\n" "Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.\n" "\n" "AutoDock is a Trade Mark of the Scripps Research Institute.\n" "\n" "This program is free software; you can redistribute it and/or\n" "modify it under the terms of the GNU General Public License\n" "as published by the Free Software Foundation; either version 2\n" "of the License, or (at your option) any later version.\n" "\n" "This program is distributed in the hope that it will be useful,\n" "but WITHOUT ANY WARRANTY; without even the implied warranty of\n" "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" "GNU General Public License for more details.\n" "\n" "You should have received a copy of the GNU General Public License\n" "along with this program; if not, write to the Free Software\n" "Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n" "\n" "*/\n" "\n" "\n" "__kernel void __attribute__ ((reqd_work_group_size(NUM_OF_THREADS_PER_BLOCK,1,1)))\n" "gpu_gen_and_eval_newpops(char dockpars_num_of_atoms,\n" " char dockpars_num_of_atypes,\n" Loading
host/src/processligand.cpp +4 −3 Original line number Diff line number Diff line Loading @@ -755,13 +755,14 @@ int get_liganddata(const char* ligfilename, Liganddata* myligand, const double A myligand->atom_rigid_structures [atom_counter] = current_rigid_struct_id; //using the id of the current rigid structure atom_counter++; #if 0 // include last atom if (atom_counter == myligand->num_of_atoms) { for (i=0; i<branch_counter; i++) //for all branches found until now if (branches [i][2] == 1) //if it is open, the atom has to be rotated atom_rotbonds_temp [atom_counter][i] = 1; //modifying atom_rotbonds_temp } #endif } if (strcmp(tempstr, "BRANCH") == 0) //if new branch, stroing atom indexes into branches [][] Loading Loading @@ -792,7 +793,7 @@ int get_liganddata(const char* ligfilename, Liganddata* myligand, const double A fscanf(fp, "%d", &(myligand->rotbonds [endbranch_counter][1])); //of endbranches (myligand->rotbonds [endbranch_counter][0])--; (myligand->rotbonds [endbranch_counter][1])--; #if 0 // include last atom before ENDBRANCH //if (atom_counter == myligand->num_of_atoms) { for (i=0; i<branch_counter; i++) //for all branches found until now Loading @@ -812,7 +813,7 @@ int get_liganddata(const char* ligfilename, Liganddata* myligand, const double A } */ // --------------------------- #endif for (i=0; i<branch_counter; i++) //the branch have to be closed if ((branches [i][0] == myligand->rotbonds [endbranch_counter][0]) && (branches [i][1] == myligand->rotbonds [endbranch_counter][1])) Loading
prebuilt/linux/ocladock_cpu_128wi +264 B (191 KiB) File changed.No diff preview for this file type. View original file View changed file
prebuilt/linux/ocladock_cpu_16wi +264 B (191 KiB) File changed.No diff preview for this file type. View original file View changed file
prebuilt/linux/ocladock_cpu_256wi +264 B (191 KiB) File changed.No diff preview for this file type. View original file View changed file
