source: src/Actions/MoleculeAction/VerletIntegrationAction.cpp@ f92ef3

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Last change on this file since f92ef3 was bcb593, checked in by Frederik Heber <heber@…>, 11 years ago

FIX: VerletIntegrationAction now assumes forces have just been calculated.

  • according to Wikipedia's Velocity_Verlet info, we first integrate position, then calculate forces, then integrate velocity. This assumes that forces based on next time step's position are already known. This is possible when parsed from file but not if they are calculated dynamically via fragmentation. Hence, we now integrate velocity from last time step to current, then integrate position from current time step to next. Then we are in the position to calculate forces and do this cycle again.
  • for this, VelocityVerletUpdate was split into ..X() and ..U() for independent integration of position and velocity.
  • VelocityVerletIntegration::operator() now first corrects forces, then integrates velocites, corrects them too and finally integrates positions according to the above new scheme.
  • removed option MDSteps from VerletIntegrationAction.
  • TESTFIX: Had to change regression rest on VerletIntegration since the cycle sequence has changed. It was nonsense before to have the forces already in some file respective to future position that actually first need to come out of the time integration.
  • Property mode set to 100644
File size: 3.4 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
5 *
6 *
7 * This file is part of MoleCuilder.
8 *
9 * MoleCuilder is free software: you can redistribute it and/or modify
10 * it under the terms of the GNU General Public License as published by
11 * the Free Software Foundation, either version 2 of the License, or
12 * (at your option) any later version.
13 *
14 * MoleCuilder is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 * GNU General Public License for more details.
18 *
19 * You should have received a copy of the GNU General Public License
20 * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
21 */
22
23/*
24 * VerletIntegrationAction.cpp
25 *
26 * Created on: May 10, 2010
27 * Author: heber
28 */
29
30// include config.h
31#ifdef HAVE_CONFIG_H
32#include <config.h>
33#endif
34
35#include "CodePatterns/MemDebug.hpp"
36
37#include "Atom/atom.hpp"
38#include "Atom/AtomSet.hpp"
39#include "CodePatterns/Log.hpp"
40#include "CodePatterns/Verbose.hpp"
41#include "Dynamics/VerletForceIntegration.hpp"
42#include "molecule.hpp"
43#include "World.hpp"
44#include "WorldTime.hpp"
45
46#include <vector>
47#include <iostream>
48#include <fstream>
49#include <string>
50
51#include "Actions/MoleculeAction/VerletIntegrationAction.hpp"
52
53using namespace MoleCuilder;
54
55// and construct the stuff
56#include "VerletIntegrationAction.def"
57#include "Action_impl_pre.hpp"
58/** =========== define the function ====================== */
59Action::state_ptr MoleculeVerletIntegrationAction::performCall() {
60 // TODO: sollte besser stream nutzen, nicht filename direkt (es sei denn, ist prefix), besser fuer unit test
61 AtomSetMixin<std::vector<atom *> > set(World::getInstance().getSelectedAtoms());
62 // we always operate relative to current time step
63 size_t CurrentStep = WorldTime::getInstance().getTime();
64 VerletForceIntegration<std::vector<atom *> > Verlet(set, params.Deltat.get(), true);
65 // parse forces into next step
66 if (!params.forcesfile.get().string().empty()) {
67 LOG(1, "Parsing forces file.");
68 if (!Verlet.parseForcesFile(params.forcesfile.get().string().c_str(), CurrentStep))
69 LOG(2, "File " << params.forcesfile.get() << " not found.");
70 else
71 LOG(2, "File " << params.forcesfile.get() << " found and parsed.");
72 }
73 // perform velocity verlet update
74 LOG(1, "Verlet integrating.");
75 if (!Verlet(CurrentStep+1, 1, 0, params.FixedCenterOfMass.get()))
76 ELOG(1, "Velocity verlet failed.");
77 else
78 LOG(2, "DEBUG: Successfully performed updates on velocity and position.");
79 // increment to next time step
80 World::getInstance().setTime(CurrentStep+1);
81
82 return Action::success;
83}
84
85Action::state_ptr MoleculeVerletIntegrationAction::performUndo(Action::state_ptr _state) {
86// MoleculeVerletIntegrationState *state = assert_cast<MoleculeVerletIntegrationState*>(_state.get());
87
88// string newName = state->mol->getName();
89// state->mol->setName(state->lastName);
90
91 return Action::failure;
92}
93
94Action::state_ptr MoleculeVerletIntegrationAction::performRedo(Action::state_ptr _state){
95 return Action::failure;
96}
97
98bool MoleculeVerletIntegrationAction::canUndo() {
99 return true;
100}
101
102bool MoleculeVerletIntegrationAction::shouldUndo() {
103 return true;
104}
105/** =========== end of function ====================== */
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