source: src/Actions/FragmentationAction/FragmentationAutomationAction.cpp@ 7d507c

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since 7d507c was b5b01e, checked in by Frederik Heber <heber@…>, 12 years ago

ActionState extracted into own header file, rename Action::state_ptr -> ActionState::ptr.

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File size: 10.8 KB
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[edecba]1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
[5aaa43]5 * Copyright (C) 2013 Frederik Heber. All rights reserved.
[94d5ac6]6 *
7 *
8 * This file is part of MoleCuilder.
9 *
10 * MoleCuilder is free software: you can redistribute it and/or modify
11 * it under the terms of the GNU General Public License as published by
12 * the Free Software Foundation, either version 2 of the License, or
13 * (at your option) any later version.
14 *
15 * MoleCuilder is distributed in the hope that it will be useful,
16 * but WITHOUT ANY WARRANTY; without even the implied warranty of
17 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18 * GNU General Public License for more details.
19 *
20 * You should have received a copy of the GNU General Public License
21 * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
[edecba]22 */
23
24/*
25 * FragmentationAutomationAction.cpp
26 *
27 * Created on: May 18, 2012
28 * Author: heber
29 */
30
31// include config.h
32#ifdef HAVE_CONFIG_H
33#include <config.h>
34#endif
35
36#include <boost/archive/text_iarchive.hpp>
37// boost asio needs specific operator new
38#include <boost/asio.hpp>
39
40#include "CodePatterns/MemDebug.hpp"
41
[a3427f]42//// include headers that implement a archive in simple text format
[55e1bc]43#include <boost/archive/text_oarchive.hpp>
44#include <boost/archive/text_iarchive.hpp>
[240c3e]45
[a3427f]46//
47//#include <boost/mpl/remove.hpp>
48//#include <boost/lambda/lambda.hpp>
[fb881a]49
[a3427f]50//#include <iostream>
[240c3e]51
[6ca578]52#include "CodePatterns/Assert.hpp"
[edecba]53#include "CodePatterns/Info.hpp"
54#include "CodePatterns/Log.hpp"
55#include "JobMarket/Jobs/FragmentJob.hpp"
56
[ac9ca4]57#include "Fragmentation/Automation/FragmentJobQueue.hpp"
[ffe057]58#include "Fragmentation/Automation/MPQCFragmentController.hpp"
[fbf143]59#include "Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp"
60#include "Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp"
[a3427f]61#include "Fragmentation/Summation/Containers/FragmentationResultContainer.hpp"
[fbf143]62#include "Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp"
63#include "Fragmentation/Summation/Containers/MPQCData.hpp"
[a3427f]64#include "Fragmentation/KeySetsContainer.hpp"
[69c733]65#ifdef HAVE_VMG
[a3427f]66#include "Fragmentation/Automation/VMGDebugGridFragmentController.hpp"
67#include "Fragmentation/Automation/VMGFragmentController.hpp"
[fbf143]68#include "Fragmentation/Summation/Containers/VMGData.hpp"
69#include "Fragmentation/Summation/Containers/VMGDataFused.hpp"
70#include "Fragmentation/Summation/Containers/VMGDataMap.hpp"
71#include "Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp"
[69c733]72#endif
[edecba]73#include "World.hpp"
74
[86cfac5]75#include <fstream>
[edecba]76#include <iostream>
77#include <string>
78#include <vector>
79
[8cae4c]80#include <boost/mpl/for_each.hpp>
81
[edecba]82#include "Actions/FragmentationAction/FragmentationAutomationAction.hpp"
83
84using namespace MoleCuilder;
85
86// and construct the stuff
87#include "FragmentationAutomationAction.def"
88#include "Action_impl_pre.hpp"
89/** =========== define the function ====================== */
90
91class controller_AddOn;
92
93// needs to be defined for using the FragmentController
94controller_AddOn *getAddOn()
95{
96 return NULL;
97}
98
[b5b01e]99ActionState::ptr FragmentationFragmentationAutomationAction::performCall() {
[c5324f]100 boost::asio::io_service io_service;
101
102 // TODO: Have io_service run in second thread and merge with current again eventually
103
[a3427f]104 FragmentationResultContainer &container =
105 FragmentationResultContainer::getInstance();
106 const KeySetsContainer& keysets = FragmentJobQueue::getInstance().getKeySets();
107 const KeySetsContainer& forcekeysets = FragmentJobQueue::getInstance().getFullKeySets();
108
[4f056e]109 size_t Exitflag = 0;
[a3427f]110 std::map<JobId_t, MPQCData> shortrangedata;
[4f056e]111 {
[ac9ca4]112 const size_t NumberJobs = FragmentJobQueue::getInstance().size();
[4f056e]113 MPQCFragmentController mpqccontroller(io_service);
114 mpqccontroller.setHost(params.host.get());
115 mpqccontroller.setPort(params.port.get());
116 // Phase One: obtain ids
[ac9ca4]117 mpqccontroller.requestIds(NumberJobs);
[4f056e]118
[ac9ca4]119 // Phase Two: add MPQCJobs and send
[503acc1]120 const size_t NoJobs = mpqccontroller.addJobsFromQueue(
[6ff62c]121 params.DoLongrange.get() ? MPQCData::DoSampleDensity : MPQCData::DontSampleDensity,
122 params.DoValenceOnly.get() ? MPQCData::DoSampleValenceOnly : MPQCData::DontSampleValenceOnly
123 );
[503acc1]124 LOG(1, "INFO: Added " << NoJobs << " from FragmentJobsQueue.");
[ac9ca4]125 mpqccontroller.run();
[4f056e]126
127 // Phase Three: calculate result
[ac9ca4]128 mpqccontroller.waitforResults(NumberJobs);
[a3427f]129 mpqccontroller.getResults(shortrangedata);
[4f056e]130
131 Exitflag += mpqccontroller.getExitflag();
132 }
[c5324f]133
[69c733]134#ifdef HAVE_VMG
135 if (params.DoLongrange.get()) {
[db6f7d]136 if ( World::getInstance().getAllAtoms().size() == 0) {
137 ELOG(1, "Please load the full molecule into the world before starting this action.");
138 return Action::failure;
139 }
[06865e]140
[849cd8]141 // obtain combined charge density
[27594e]142 FragmentationChargeDensity summedChargeDensity(
[a3427f]143 shortrangedata,
[bae7bc]144 FragmentJobQueue::getInstance().getKeySets());
[27594e]145 const std::vector<SamplingGrid> full_sample = summedChargeDensity.getFullSampledGrid();
[a3427f]146 LOG(1, "INFO: There are " << shortrangedata.size() << " short-range and "
[4f056e]147 << full_sample.size() << " level-wise long-range jobs.");
[69c733]148
[1e5f84]149 // check boundary conditions
150 const BoundaryConditions::Conditions_t &conditions =
151 World::getInstance().getDomain().getConditions();
152 const bool OpenBoundaryConditions =
153 !((conditions[0] == BoundaryConditions::Wrap) &&
154 (conditions[1] == BoundaryConditions::Wrap) &&
155 (conditions[2] == BoundaryConditions::Wrap));
156 LOG(1, std::string("INFO: Using ")
157 << (OpenBoundaryConditions ? "open" : "periodic")
158 << " boundary conditions.");
159
[4f056e]160 // Phase Four: obtain more ids
[a3427f]161 std::map<JobId_t, VMGData> longrangedata;
[4f056e]162 {
163 VMGFragmentController vmgcontroller(io_service);
164 vmgcontroller.setHost(params.host.get());
165 vmgcontroller.setPort(params.port.get());
[a3427f]166 const size_t NoJobs = shortrangedata.size()+full_sample.size();
[e2925fd]167 vmgcontroller.requestIds(2*NoJobs);
[4f056e]168
[e2925fd]169 // Phase Five a: create VMGJobs for electronic charge distribution
[4f056e]170 const size_t near_field_cells = params.near_field_cells.get();
[cd2591]171 const size_t interpolation_degree = params.interpolation_degree.get();
[4f056e]172 if (!vmgcontroller.createLongRangeJobs(
[a3427f]173 shortrangedata,
[4f056e]174 full_sample,
[cd2591]175 near_field_cells,
[6ff62c]176 interpolation_degree,
[e2925fd]177 VMGFragmentController::DontSampleParticles,
178 VMGFragmentController::DoTreatGrid,
[b6b21a]179 params.DoValenceOnly.get() ? MPQCData::DoSampleValenceOnly : MPQCData::DontSampleValenceOnly,
[1e5f84]180 params.DoPrintDebug.get(),
181 OpenBoundaryConditions))
[4f056e]182 return Action::failure;
183
[e2925fd]184 // Phase Six a: calculate result
[4f056e]185 vmgcontroller.waitforResults(NoJobs);
[a3427f]186 vmgcontroller.getResults(longrangedata);
187 ASSERT( NoJobs == longrangedata.size(),
[4f056e]188 "FragmentationFragmentationAutomationAction::performCall() - number of MPQCresults+"
189 +toString(full_sample.size())+"="+toString(NoJobs)
[e2925fd]190 +" and first VMGresults "+toString(longrangedata.size())+" don't match.");
[4f056e]191 Exitflag += vmgcontroller.getExitflag();
[e2925fd]192
193 {
194 std::map<JobId_t, VMGData> longrangedata_both;
195 // Phase Five b: create VMGJobs for nuclei charge distributions
196 const size_t near_field_cells = params.near_field_cells.get();
197 const size_t interpolation_degree = params.interpolation_degree.get();
198 if (!vmgcontroller.createLongRangeJobs(
199 shortrangedata,
200 full_sample,
201 near_field_cells,
202 interpolation_degree,
203 VMGFragmentController::DoSampleParticles,
204 VMGFragmentController::DoTreatGrid,
205 params.DoValenceOnly.get() ? MPQCData::DoSampleValenceOnly : MPQCData::DontSampleValenceOnly,
[1e5f84]206 params.DoPrintDebug.get(),
207 OpenBoundaryConditions))
[e2925fd]208 return Action::failure;
209
210 // Phase Six b: calculate result
211 vmgcontroller.waitforResults(NoJobs);
212 vmgcontroller.getResults(longrangedata_both);
213 ASSERT( NoJobs == longrangedata_both.size(),
214 "FragmentationFragmentationAutomationAction::performCall() - number of MPQCresults+"
215 +toString(full_sample.size())+"="+toString(NoJobs)
216 +" and second VMGresults "+toString(longrangedata_both.size())+" don't match.");
217 Exitflag += vmgcontroller.getExitflag();
218
219 // go through either data and replace nuclei_long with contribution from both
220 ASSERT( longrangedata.size() == longrangedata_both.size(),
221 "FragmentationFragmentationAutomationAction::performCall() - longrange results have different sizes.");
222 std::map<JobId_t, VMGData>::iterator destiter = longrangedata.begin();
[e355b31]223 std::map<JobId_t, VMGData>::const_iterator srciter = longrangedata_both.begin();
224 for (;destiter != longrangedata.end(); ++srciter, ++destiter) {
225 destiter->second.both_sampled_potential = srciter->second.sampled_potential;
[e2925fd]226 destiter->second.nuclei_long = srciter->second.nuclei_long;
[e355b31]227 }
[e2925fd]228 }
[4f056e]229 }
[a2295a]230
[b6b21a]231 if (params.DoPrintDebug.get()) {
232 std::map<JobId_t, std::string> debugData;
233 {
234 if (!full_sample.empty()) {
235 // create debug jobs for each level to print the summed-up potential to vtk files
236 VMGDebugGridFragmentController debugcontroller(io_service);
237 debugcontroller.setHost(params.host.get());
238 debugcontroller.setPort(params.port.get());
239 debugcontroller.requestIds(full_sample.size());
[1e5f84]240 if (!debugcontroller.createDebugJobs(full_sample, OpenBoundaryConditions))
[b6b21a]241 return Action::failure;
242 debugcontroller.waitforResults(full_sample.size());
243 debugcontroller.getResults(debugData);
244 Exitflag += debugcontroller.getExitflag();
245 }
[a2295a]246 }
[2764e0]247 }
[a3427f]248 container.addFullResults(keysets, forcekeysets, shortrangedata, longrangedata);
249 } else {
250 container.addShortRangeResults(keysets, forcekeysets, shortrangedata);
[69c733]251 }
[a3427f]252#else
253 container.addShortRangeResults(keysets, forcekeysets, shortrangedata);
[69c733]254#endif
[edecba]255
[bae7bc]256 // now clear all present jobs as we are done
257 FragmentJobQueue::getInstance().clear();
258
[55e1bc]259 // if file is given, advise results container to store to file
260 if (!params.resultsfile.get().empty()) {
261 boost::filesystem::path resultsfile = params.resultsfile.get();
262 std::ofstream returnstream(resultsfile.string().c_str());
263 if (returnstream.good()) {
264 boost::archive::text_oarchive oa(returnstream);
265 oa << container;
266 }
267 Exitflag += (int)(!returnstream.good());
268 returnstream.close();
269 }
270
[edecba]271 return (Exitflag == 0) ? Action::success : Action::failure;
272}
273
[b5b01e]274ActionState::ptr FragmentationFragmentationAutomationAction::performUndo(ActionState::ptr _state) {
[edecba]275 return Action::success;
276}
277
[b5b01e]278ActionState::ptr FragmentationFragmentationAutomationAction::performRedo(ActionState::ptr _state){
[edecba]279 return Action::success;
280}
281
282bool FragmentationFragmentationAutomationAction::canUndo() {
283 return false;
284}
285
286bool FragmentationFragmentationAutomationAction::shouldUndo() {
287 return false;
288}
289/** =========== end of function ====================== */
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