source: src/Parser/PcpParser.hpp@ bdc91e

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 Candidate_v1.7.0 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 bdc91e was 35b698, checked in by Frederik Heber <heber@…>, 15 years ago

BIG CHANGE: config::load and config::save in ParseCommandLineOptions() and main() replaced with FormatParser replacements.

Fragmentation:

  • FIX: MoleculeFillWithMoleculeAction: filler atoms have to be removed before the system can be stored to file.
  • FIX: PcpParser::load() - has to put the molecule also into World's MoleculeListClass (otherwise the name cannot be set right after loading)
  • new Libparser.a
  • all sources from PARSER subdir are compiled into libparser such that only ParserUnitTest is recompiled.

Testfixes:

  • testsuite-fragmentation - changes to due to different -f calling syntax.
  • most of the xyz files had to be replaced due to a single whitespace at the end of each entry: Domain/6, Simple_configuration/2, Simple_configuration/3, Simple_configuration/4, Simple_configuration/5, Simple_configuration/8
  • in many cases were the number orbitals (and thus MaxMinStopStep) wrong: Filling/1, Simple_configuration/4, Simple_configuration/5

Signed-off-by: Frederik Heber <heber@…>
  • Property mode set to 100644
File size: 2.6 KB
RevLine 
[43dad6]1/*
2 * PcpParser.hpp
3 *
4 * Created on: 12.06.2010
5 * Author: heber
6 */
7
8#ifndef PCPPARSER_HPP_
9#define PCPPARSER_HPP_
10
11#include <iostream>
[650ca8c]12#include "Parser/FormatParser.hpp"
[43dad6]13
14/**
15 * Parser for PCP config files.
16 */
17class PcpParser : public FormatParser {
18public:
19 PcpParser();
20 ~PcpParser();
21 void load(std::istream* file);
22 void save(std::ostream* file);
23
[1b2d30]24 bool operator==(const PcpParser& b) const;
25
[43dad6]26private:
27
28 void ParseThermostats(class ConfigFileBuffer * const fb);
29 void OutputAtoms(ostream *file, vector<atom *> &allatoms, map<int, int> &ZtoIndexMap);
30 void OutputElements(ostream *file, vector<atom *> &allatoms, map<int, int> &ZtoIndexMap);
[650ca8c]31 void CalculateOrbitals(vector<atom *> &allatoms);
[43dad6]32
33 struct StructParallelization {
34 int ProcPEGamma;
35 int ProcPEPsi;
36 } Parallelization;
37
38 /*
39 * Contains all the paths and names
40 */
41 struct StructPaths {
42 char *databasepath;
43 char *configname;
44 char *mainname;
45 char *defaultpath;
46 char *pseudopotpath;
47 } Paths;
48
49 /*
50 * Contains all Do/Don't switches
51 */
52 struct StructSwitches {
53 int DoConstrainedMD;
54 int DoOutVis;
55 int DoOutMes;
56 int DoOutNICS;
57 int DoOutOrbitals;
58 int DoOutCurrent;
59 int DoFullCurrent;
60 int DoPerturbation;
61 int DoWannier;
62 } Switches;
63
64 /*
65 * Contains parameters regarding localization of orbitals or magnetic perturbation
66 */
67 struct StructLocalizedOrbitals {
68 int CommonWannier;
69 double SawtoothStart;
70 int VectorPlane;
71 double VectorCut;
72 int UseAddGramSch;
73 int Seed;
74 double EpsWannier;
75 } LocalizedOrbitals;
76
77 /*
78 * Contains all step count and other epsilon threshold parameters
79 */
80 struct StructStepCounts {
81 int MaxMinStopStep;
82 int InitMaxMinStopStep;
83
84 int OutVisStep;
85 int OutSrcStep;
86 int MaxPsiStep;
87
88 int MaxOuterStep;
89
90 int MaxMinStep;
91 double RelEpsTotalEnergy;
92 double RelEpsKineticEnergy;
93 int MaxMinGapStopStep;
94 int MaxInitMinStep;
95 double InitRelEpsTotalEnergy;
96 double InitRelEpsKineticEnergy;
97 int InitMaxMinGapStopStep;
98 } StepCounts;
99
100 /*
101 * Contains all parameters specific to the plane wave basis set
102 */
103 struct StructPlaneWaveSpecifics {
104 int PsiType;
105 int MaxPsiDouble;
106 int PsiMaxNoUp;
107 int PsiMaxNoDown;
108 double ECut;
109 int MaxLevel;
110 int RiemannTensor;
111 int LevRFactor;
112 int RiemannLevel;
113 int Lev0Factor;
114 int RTActualUse;
115 int AddPsis;
116 double RCut;
117 } PlaneWaveSpecifics;
118
119 bool FastParsing;
120
121 double Deltat;
122 int IsAngstroem;
123 int RelativeCoord;
124 int StructOpt;
125 int MaxTypes;
126 string basis;
127};
128
129#endif /* PCPPARSER_HPP_ */
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