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