Action_Thermostats
Add_AtomRandomPerturbation
Add_RotateAroundBondAction
Add_SelectAtomByNameAction
Adding_Graph_to_ChangeBondActions
Adding_MD_integration_tests
Adding_StructOpt_integration_tests
AutomationFragmentation_failures
Candidate_v1.6.0
Candidate_v1.6.1
ChangeBugEmailaddress
ChangingTestPorts
ChemicalSpaceEvaluator
Combining_Subpackages
Debian_Package_split
Debian_package_split_molecuildergui_only
Disabling_MemDebug
Docu_Python_wait
EmpiricalPotential_contain_HomologyGraph_documentation
Enable_parallel_make_install
Enhance_userguide
Enhanced_StructuralOptimization
Enhanced_StructuralOptimization_continued
Example_ManyWaysToTranslateAtom
Exclude_Hydrogens_annealWithBondGraph
FitPartialCharges_GlobalError
Fix_ChronosMutex
Fix_StatusMsg
Fix_StepWorldTime_single_argument
Fix_Verbose_Codepatterns
ForceAnnealing_goodresults
ForceAnnealing_oldresults
ForceAnnealing_tocheck
ForceAnnealing_with_BondGraph
ForceAnnealing_with_BondGraph_continued
ForceAnnealing_with_BondGraph_continued_betteresults
ForceAnnealing_with_BondGraph_contraction-expansion
GeometryObjects
Gui_displays_atomic_force_velocity
IndependentFragmentGrids_IntegrationTest
JobMarket_RobustOnKillsSegFaults
JobMarket_StableWorkerPool
JobMarket_unresolvable_hostname_fix
ODR_violation_mpqc_open
PartialCharges_OrthogonalSummation
PythonUI_with_named_parameters
QtGui_reactivate_TimeChanged_changes
Recreated_GuiChecks
RotateToPrincipalAxisSystem_UndoRedo
StoppableMakroAction
Subpackage_levmar
Subpackage_vmg
ThirdParty_MPQC_rebuilt_buildsystem
TremoloParser_IncreasedPrecision
TremoloParser_MultipleTimesteps
Ubuntu_1604_changes
stable
| Line | |
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| 1 |
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| 2 | #ifdef __GNUG__
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| 3 | #pragma implementation
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| 4 | #endif
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| 5 |
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| 6 | #include <iostream>
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| 7 |
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| 8 | #include <util/misc/formio.h>
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| 9 | #include <chemistry/molecule/molecule.h>
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| 10 | #include <chemistry/molecule/atominfo.h>
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| 11 | #include <chemistry/qc/psi/psiexenv.h>
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| 12 | #include <chemistry/qc/psi/psifile11.h>
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| 13 |
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| 14 | using namespace std;
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| 15 |
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| 16 | namespace sc {
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| 17 |
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| 18 | PsiFile11::PsiFile11(const string& name) : file_()
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| 19 | {
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| 20 | filename_ = string(name);
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| 21 | }
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| 22 |
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| 23 | PsiFile11::~PsiFile11()
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| 24 | {
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| 25 | }
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| 26 |
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| 27 | void
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| 28 | PsiFile11::rewind()
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| 29 | {
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| 30 | file_.seekg(0,ios::beg);
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| 31 | }
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| 32 |
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| 33 | void
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| 34 | PsiFile11::skip_lines(int n)
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| 35 | {
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| 36 | // Lines in File11 are guaranteed to be 80 characters
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| 37 | char line[100];
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| 38 | for(int i=0; i<n; i++)
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| 39 | file_.getline(line,100);
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| 40 | }
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| 41 |
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| 42 | void
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| 43 | PsiFile11::skip_entry()
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| 44 | {
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| 45 | skip_lines(1);
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| 46 | int natom;
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| 47 | file_ >> natom;
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| 48 | double energy;
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| 49 | file_ >> energy;
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| 50 | skip_lines(2*natom);
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| 51 | }
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| 52 |
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| 53 | void
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| 54 | PsiFile11::open()
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| 55 | {
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| 56 | file_.open(filename_.c_str(),ios::in);
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| 57 | }
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| 58 |
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| 59 | void
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| 60 | PsiFile11::close()
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| 61 | {
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| 62 | if (!file_.is_open())
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| 63 | file_.close();
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| 64 | }
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| 65 |
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| 66 | void
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| 67 | PsiFile11::remove()
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| 68 | {
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| 69 | if (file_.is_open())
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| 70 | file_.close();
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| 71 | file_.open(filename_.c_str(),ios::out | ios::trunc);
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| 72 | file_.close();
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| 73 | }
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| 74 |
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| 75 | int
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| 76 | PsiFile11::get_natom(int entry)
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| 77 | {
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| 78 | skip_lines(1);
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| 79 |
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| 80 | int natom;
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| 81 | file_ >> natom;
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| 82 | rewind();
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| 83 | return natom;
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| 84 | }
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| 85 |
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| 86 | double
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| 87 | PsiFile11::get_energy(int entry)
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| 88 | {
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| 89 | skip_lines(1);
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| 90 |
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| 91 | int natom;
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| 92 | file_ >> natom;
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| 93 | double energy;
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| 94 | file_ >> energy;
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| 95 | rewind();
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| 96 | return energy;
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| 97 | }
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| 98 |
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| 99 | double
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| 100 | PsiFile11::get_coord(int entry, int atom, int xyz)
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| 101 | {
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| 102 | skip_lines(1);
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| 103 | int natom;
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| 104 | file_ >> natom;
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| 105 | if (natom <= atom)
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| 106 | abort();
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| 107 | double energy;
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| 108 | file_ >> energy;
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| 109 |
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| 110 | skip_lines(atom+1);
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| 111 | double charge;
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| 112 | file_ >> charge;
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| 113 | double trash;
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| 114 | for(int i=0; i<xyz; i++)
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| 115 | file_ >> trash;
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| 116 | double coord;
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| 117 | file_ >> coord;
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| 118 |
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| 119 | rewind();
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| 120 | return coord;
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| 121 | }
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| 122 |
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| 123 | double
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| 124 | PsiFile11::get_grad(int entry, int atom, int xyz)
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| 125 | {
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| 126 | skip_lines(1);
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| 127 | int natom;
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| 128 | file_ >> natom;
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| 129 | if (natom <= atom)
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| 130 | abort();
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| 131 | double energy;
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| 132 | file_ >> energy;
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| 133 |
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| 134 | skip_lines(natom+atom+1);
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| 135 | double trash;
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| 136 | for(int i=0; i<xyz; i++)
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| 137 | file_ >> trash;
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| 138 | double grad;
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| 139 | file_ >> grad;
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| 140 |
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| 141 | rewind();
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| 142 | return grad;
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| 143 | }
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| 144 |
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| 145 | }
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