| 1 | /** \file config.cpp
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| 2 |  * 
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| 3 |  * Function implementations for the class config.
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| 4 |  * 
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| 5 |  */
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| 6 | 
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| 7 | #include "molecules.hpp"
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| 8 | 
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| 9 | /************************************* Functions for class config ***************************/
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| 10 | 
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| 11 | /** Constructor for config file class.
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| 12 |  */
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| 13 | config::config()
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| 14 | {
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| 15 |   mainname = (char *) MallocString(sizeof(char)*MAXSTRINGSIZE,"config constructor: mainname");
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| 16 |   defaultpath = (char *) MallocString(sizeof(char)*MAXSTRINGSIZE,"config constructor: mainname");
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| 17 |   pseudopotpath = (char *) MallocString(sizeof(char)*MAXSTRINGSIZE,"config constructor: mainname");
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| 18 |   configpath = (char *) MallocString(sizeof(char)*MAXSTRINGSIZE,"config constructor: mainname");
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| 19 |   configname = (char *) MallocString(sizeof(char)*MAXSTRINGSIZE,"config constructor: mainname");
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| 20 |   ThermostatImplemented = (int *) Malloc((MaxThermostats)*(sizeof(int)), "IonsInitRead: *ThermostatImplemented");
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| 21 |   ThermostatNames = (char **) Malloc((MaxThermostats)*(sizeof(char *)), "IonsInitRead: *ThermostatNames");
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| 22 |   for (int j=0;j<MaxThermostats;j++)
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| 23 |     ThermostatNames[j] = (char *) MallocString(12*(sizeof(char)), "IonsInitRead: ThermostatNames[]");
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| 24 |   Thermostat = 4;
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| 25 |   alpha = 0.;
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| 26 |   ScaleTempStep = 25;
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| 27 |   TempFrequency = 2.5;
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| 28 |   strcpy(mainname,"pcp");
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| 29 |   strcpy(defaultpath,"not specified");
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| 30 |   strcpy(pseudopotpath,"not specified");
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| 31 |   configpath[0]='\0';
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| 32 |   configname[0]='\0';
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| 33 | 
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| 34 |   strcpy(ThermostatNames[0],"None");
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| 35 |   ThermostatImplemented[0] = 1;
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| 36 |   strcpy(ThermostatNames[1],"Woodcock"); 
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| 37 |   ThermostatImplemented[1] = 1;
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| 38 |   strcpy(ThermostatNames[2],"Gaussian"); 
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| 39 |   ThermostatImplemented[2] = 1;
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| 40 |   strcpy(ThermostatNames[3],"Langevin"); 
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| 41 |   ThermostatImplemented[3] = 1;
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| 42 |   strcpy(ThermostatNames[4],"Berendsen"); 
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| 43 |   ThermostatImplemented[4] = 1;
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| 44 |   strcpy(ThermostatNames[5],"NoseHoover"); 
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| 45 |   ThermostatImplemented[5] = 1;
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| 46 | 
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| 47 |   FastParsing = false;
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| 48 |   ProcPEGamma=8;
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| 49 |   ProcPEPsi=1;
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| 50 |   DoOutVis=0;
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| 51 |   DoOutMes=1;
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| 52 |   DoOutNICS=0;
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| 53 |   DoOutOrbitals=0;
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| 54 |   DoOutCurrent=0;
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| 55 |   DoPerturbation=0;
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| 56 |   DoFullCurrent=0;
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| 57 |   DoWannier=0;
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| 58 |   DoConstrainedMD=0;
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| 59 |   CommonWannier=0;
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| 60 |   SawtoothStart=0.01;
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| 61 |   VectorPlane=0;
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| 62 |   VectorCut=0;
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| 63 |   UseAddGramSch=1;
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| 64 |   Seed=1;
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| 65 |   MaxOuterStep=0;
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| 66 |   Deltat=0.01;
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| 67 |   OutVisStep=10;
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| 68 |   OutSrcStep=5;
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| 69 |   TargetTemp=0.00095004455;
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| 70 |   ScaleTempStep=25;
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| 71 |   MaxPsiStep=0;
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| 72 |   EpsWannier=1e-7;
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| 73 |   
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| 74 |   MaxMinStep=100;
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| 75 |   RelEpsTotalEnergy=1e-7;
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| 76 |   RelEpsKineticEnergy=1e-5;
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| 77 |   MaxMinStopStep=1;
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| 78 |   MaxMinGapStopStep=0;
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| 79 |   MaxInitMinStep=100;
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| 80 |   InitRelEpsTotalEnergy=1e-5;
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| 81 |   InitRelEpsKineticEnergy=1e-4;
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| 82 |   InitMaxMinStopStep=1;
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| 83 |   InitMaxMinGapStopStep=0;
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| 84 |   
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| 85 |   //BoxLength[NDIM*NDIM];
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| 86 |   
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| 87 |   ECut=128.;
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| 88 |   MaxLevel=5;
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| 89 |   RiemannTensor=0;
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| 90 |   LevRFactor=0;
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| 91 |   RiemannLevel=0;
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| 92 |   Lev0Factor=2;
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| 93 |   RTActualUse=0;
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| 94 |   PsiType=0;
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| 95 |   MaxPsiDouble=0;
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| 96 |   PsiMaxNoUp=0;
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| 97 |   PsiMaxNoDown=0;
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| 98 |   AddPsis=0;
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| 99 |   
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| 100 |   RCut=20.;
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| 101 |   StructOpt=0;
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| 102 |   IsAngstroem=1;
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| 103 |   RelativeCoord=0;
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| 104 |   MaxTypes=0;
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| 105 | };
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| 106 | 
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| 107 | 
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| 108 | /** Destructor for config file class.
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| 109 |  */
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| 110 | config::~config()
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| 111 | {
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| 112 |   Free((void **)&mainname, "config::~config: *mainname");
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| 113 |   Free((void **)&defaultpath, "config::~config: *defaultpath");
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| 114 |   Free((void **)&pseudopotpath, "config::~config: *pseudopotpath");
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| 115 |   Free((void **)&configpath, "config::~config: *configpath");
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| 116 |   Free((void **)&configname, "config::~config: *configname");
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| 117 | };
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| 118 | 
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| 119 | /** Readin of Thermostat related values from parameter file.
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| 120 |  * \param *source parameter file
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| 121 |  */
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| 122 | void config::InitThermostats(ifstream *source)
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| 123 | {
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| 124 |   char *thermo = MallocString(12, "IonsInitRead: thermo");
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| 125 |   int verbose = 0;
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| 126 | 
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| 127 |   // read desired Thermostat from file along with needed additional parameters
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| 128 |   if (ParseForParameter(verbose,source,"Thermostat", 0, 1, 1, string_type, thermo, 1, optional)) {
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| 129 |     if (strcmp(thermo, ThermostatNames[0]) == 0) { // None
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| 130 |       if (ThermostatImplemented[0] == 1) {
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| 131 |         Thermostat = None;
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| 132 |       } else {
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| 133 |         cout << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
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| 134 |         Thermostat = None;
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| 135 |       }
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| 136 |     } else if (strcmp(thermo, ThermostatNames[1]) == 0) { // Woodcock
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| 137 |       if (ThermostatImplemented[1] == 1) {
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| 138 |         Thermostat = Woodcock;
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| 139 |         ParseForParameter(verbose,source,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read scaling frequency
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| 140 |       } else {
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| 141 |         cout << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
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| 142 |         Thermostat = None;
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| 143 |       }
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| 144 |     } else if (strcmp(thermo, ThermostatNames[2]) == 0) { // Gaussian
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| 145 |       if (ThermostatImplemented[2] == 1) {
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| 146 |         Thermostat = Gaussian;
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| 147 |         ParseForParameter(verbose,source,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read collision rate
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| 148 |       } else {
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| 149 |         cout << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
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| 150 |         Thermostat = None;
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| 151 |       }
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| 152 |     } else if (strcmp(thermo, ThermostatNames[3]) == 0) { // Langevin
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| 153 |       if (ThermostatImplemented[3] == 1) {
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| 154 |         Thermostat = Langevin;
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| 155 |         ParseForParameter(verbose,source,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read gamma
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| 156 |         if (ParseForParameter(verbose,source,"Thermostat", 0, 3, 1, double_type, &alpha, 1, optional)) {
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| 157 |           cout << Verbose(2) << "Extended Stochastic Thermostat detected with interpolation coefficient " << alpha << "." << endl;
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| 158 |         } else {
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| 159 |           alpha = 1.;
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| 160 |         }
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| 161 |       } else {
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| 162 |         cout << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
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| 163 |         Thermostat = None;
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| 164 |       }
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| 165 |     } else if (strcmp(thermo, ThermostatNames[4]) == 0) { // Berendsen
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| 166 |       if (ThermostatImplemented[4] == 1) {
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| 167 |         Thermostat = Berendsen;
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| 168 |         ParseForParameter(verbose,source,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read \tau_T
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| 169 |       } else {
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| 170 |         cout << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
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| 171 |         Thermostat = None;
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| 172 |       }
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| 173 |     } else if (strcmp(thermo, ThermostatNames[5]) == 0) { // Nose-Hoover
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| 174 |       if (ThermostatImplemented[5] == 1) {
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| 175 |         Thermostat = NoseHoover;
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| 176 |         ParseForParameter(verbose,source,"Thermostat", 0, 2, 1, double_type, &HooverMass, 1, critical); // read Hoovermass
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| 177 |         alpha = 0.;
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| 178 |       } else {
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| 179 |         cout << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
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| 180 |         Thermostat = None;
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| 181 |       }
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| 182 |     } else {
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| 183 |       cout << Verbose(1) << " Warning: thermostat name was not understood!" << endl;
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| 184 |       Thermostat = None;
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| 185 |     }
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| 186 |   } else {
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| 187 |     if ((MaxOuterStep > 0) && (TargetTemp != 0)) 
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| 188 |       cout << Verbose(2) <<  "No thermostat chosen despite finite temperature MD, falling back to None." << endl;
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| 189 |     Thermostat = None;
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| 190 |   }
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| 191 |   Free((void **)&thermo, "InitThermostats: thermo");
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| 192 | };
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| 193 | 
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| 194 | 
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| 195 | /** Displays menu for editing each entry of the config file.
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| 196 |  * Nothing fancy here, just lots of cout << Verbose(0)s for the menu and a switch/case
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| 197 |  * for each entry of the config file structure.
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| 198 |  */
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| 199 | void config::Edit(molecule *mol)
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| 200 | {
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| 201 |   char choice;
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| 202 |   
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| 203 |   do {
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| 204 |     cout << Verbose(0) << "===========EDIT CONFIGURATION============================" << endl;
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| 205 |     cout << Verbose(0) << " A - mainname (prefix for all runtime files)" << endl;
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| 206 |     cout << Verbose(0) << " B - Default path (for runtime files)" << endl;
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| 207 |     cout << Verbose(0) << " C - Path of pseudopotential files" << endl;
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| 208 |     cout << Verbose(0) << " D - Number of coefficient sharing processes" << endl;
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| 209 |     cout << Verbose(0) << " E - Number of wave function sharing processes" << endl;
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| 210 |     cout << Verbose(0) << " F - 0: Don't output density for OpenDX, 1: do" << endl;
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| 211 |     cout << Verbose(0) << " G - 0: Don't output physical data, 1: do" << endl;
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| 212 |     cout << Verbose(0) << " H - 0: Don't output densities of each unperturbed orbital for OpenDX, 1: do" << endl;
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| 213 |     cout << Verbose(0) << " I - 0: Don't output current density for OpenDX, 1: do" << endl;
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| 214 |     cout << Verbose(0) << " J - 0: Don't do the full current calculation, 1: do" << endl;
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| 215 |     cout << Verbose(0) << " K - 0: Don't do perturbation calculation to obtain susceptibility and shielding, 1: do" << endl;
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| 216 |     cout << Verbose(0) << " L - 0: Wannier centres as calculated, 1: common centre for all, 2: unite centres according to spread, 3: cell centre, 4: shifted to nearest grid point" << endl;
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| 217 |     cout << Verbose(0) << " M - Absolute begin of unphysical sawtooth transfer for position operator within cell" << endl;
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| 218 |     cout << Verbose(0) << " N - (0,1,2) x,y,z-plane to do two-dimensional current vector cut" << endl;
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| 219 |     cout << Verbose(0) << " O - Absolute position along vector cut axis for cut plane" << endl;
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| 220 |     cout << Verbose(0) << " P - Additional Gram-Schmidt-Orthonormalization to stabilize numerics" << endl;
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| 221 |     cout << Verbose(0) << " Q - Initial integer value of random number generator" << endl;
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| 222 |     cout << Verbose(0) << " R - for perturbation 0, for structure optimization defines upper limit of iterations" << endl;
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| 223 |     cout << Verbose(0) << " T - Output visual after ...th step" << endl;
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| 224 |     cout << Verbose(0) << " U - Output source densities of wave functions after ...th step" << endl;
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| 225 |     cout << Verbose(0) << " X - minimization iterations per wave function, if unsure leave at default value 0" << endl;
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| 226 |     cout << Verbose(0) << " Y - tolerance value for total spread in iterative Jacobi diagonalization" << endl;
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| 227 |     cout << Verbose(0) << " Z - Maximum number of minimization iterations" << endl;
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| 228 |     cout << Verbose(0) << " a - Relative change in total energy to stop min. iteration" << endl;
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| 229 |     cout << Verbose(0) << " b - Relative change in kinetic energy to stop min. iteration" << endl;
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| 230 |     cout << Verbose(0) << " c - Check stop conditions every ..th step during min. iteration" << endl;
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| 231 |     cout << Verbose(0) << " e - Maximum number of minimization iterations during initial level" << endl;
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| 232 |     cout << Verbose(0) << " f - Relative change in total energy to stop min. iteration during initial level" << endl;
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| 233 |     cout << Verbose(0) << " g - Relative change in kinetic energy to stop min. iteration during initial level" << endl;
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| 234 |     cout << Verbose(0) << " h - Check stop conditions every ..th step during min. iteration during initial level" << endl;
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| 235 |     cout << Verbose(0) << " j - six lower diagonal entries of matrix, defining the unit cell" << endl;
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| 236 |     cout << Verbose(0) << " k - Energy cutoff of plane wave basis in Hartree" << endl;
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| 237 |     cout << Verbose(0) << " l - Maximum number of levels in multi-level-ansatz" << endl;
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| 238 |     cout << Verbose(0) << " m - Factor by which grid nodes increase between standard and upper level" << endl;
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| 239 |     cout << Verbose(0) << " n - 0: Don't use RiemannTensor, 1: Do" << endl;
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| 240 |     cout << Verbose(0) << " o - Factor by which grid nodes increase between Riemann and standard(?) level" << endl;
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| 241 |     cout << Verbose(0) << " p - Number of Riemann levels" << endl;
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| 242 |     cout << Verbose(0) << " r - 0: Don't Use RiemannTensor, 1: Do" << endl;
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| 243 |     cout << Verbose(0) << " s - 0: Doubly occupied orbitals, 1: Up-/Down-Orbitals" << endl;
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| 244 |     cout << Verbose(0) << " t - Number of orbitals (depends pn SpinType)" << endl;
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| 245 |     cout << Verbose(0) << " u - Number of SpinUp orbitals (depends on SpinType)" << endl;
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| 246 |     cout << Verbose(0) << " v - Number of SpinDown orbitals (depends on SpinType)" << endl;
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| 247 |     cout << Verbose(0) << " w - Number of additional, unoccupied orbitals" << endl;
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| 248 |     cout << Verbose(0) << " x - radial cutoff for ewald summation in Bohrradii" << endl;
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| 249 |     cout << Verbose(0) << " y - 0: Don't do structure optimization beforehand, 1: Do" << endl;
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| 250 |     cout << Verbose(0) << " z - 0: Units are in Bohr radii, 1: units are in Aengstrom" << endl;
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| 251 |     cout << Verbose(0) << " i - 0: Coordinates given in file are absolute, 1: ... are relative to unit cell" << endl;
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| 252 |     cout << Verbose(0) << "=========================================================" << endl;
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| 253 |     cout << Verbose(0) << "INPUT: ";
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| 254 |     cin >> choice;
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| 255 |     
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| 256 |     switch (choice) {
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| 257 |         case 'A': // mainname
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| 258 |           cout << Verbose(0) << "Old: " << config::mainname << "\t new: ";
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| 259 |           cin >> config::mainname;
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| 260 |           break;
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| 261 |         case 'B': // defaultpath
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| 262 |           cout << Verbose(0) << "Old: " << config::defaultpath << "\t new: ";
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| 263 |           cin >> config::defaultpath;
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| 264 |           break;
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| 265 |         case 'C': // pseudopotpath
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| 266 |           cout << Verbose(0) << "Old: " << config::pseudopotpath << "\t new: ";
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| 267 |           cin >> config::pseudopotpath;
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| 268 |           break;
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| 269 | 
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| 270 |         case 'D': // ProcPEGamma
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| 271 |           cout << Verbose(0) << "Old: " << config::ProcPEGamma << "\t new: ";
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| 272 |           cin >> config::ProcPEGamma;
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| 273 |           break;
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| 274 |         case 'E': // ProcPEPsi
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| 275 |           cout << Verbose(0) << "Old: " << config::ProcPEPsi << "\t new: ";
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| 276 |           cin >> config::ProcPEPsi;
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| 277 |           break;
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| 278 |         case 'F': // DoOutVis
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| 279 |           cout << Verbose(0) << "Old: " << config::DoOutVis << "\t new: ";
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| 280 |           cin >> config::DoOutVis;
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| 281 |           break;
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| 282 |         case 'G': // DoOutMes
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| 283 |           cout << Verbose(0) << "Old: " << config::DoOutMes << "\t new: ";
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| 284 |           cin >> config::DoOutMes;
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| 285 |           break;
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| 286 |         case 'H': // DoOutOrbitals
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| 287 |           cout << Verbose(0) << "Old: " << config::DoOutOrbitals << "\t new: ";
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| 288 |           cin >> config::DoOutOrbitals;
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| 289 |           break;
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| 290 |         case 'I': // DoOutCurrent
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| 291 |           cout << Verbose(0) << "Old: " << config::DoOutCurrent << "\t new: ";
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| 292 |           cin >> config::DoOutCurrent;
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| 293 |           break;
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| 294 |         case 'J': // DoFullCurrent
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| 295 |           cout << Verbose(0) << "Old: " << config::DoFullCurrent << "\t new: ";
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| 296 |           cin >> config::DoFullCurrent;
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| 297 |           break;
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| 298 |         case 'K': // DoPerturbation
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| 299 |           cout << Verbose(0) << "Old: " << config::DoPerturbation << "\t new: ";
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| 300 |           cin >> config::DoPerturbation;
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| 301 |           break;
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| 302 |         case 'L': // CommonWannier
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| 303 |           cout << Verbose(0) << "Old: " << config::CommonWannier << "\t new: ";
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| 304 |           cin >> config::CommonWannier;
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| 305 |           break;
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| 306 |         case 'M': // SawtoothStart
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| 307 |           cout << Verbose(0) << "Old: " << config::SawtoothStart << "\t new: ";
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| 308 |           cin >> config::SawtoothStart;
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| 309 |           break;
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| 310 |         case 'N': // VectorPlane
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| 311 |           cout << Verbose(0) << "Old: " << config::VectorPlane << "\t new: ";
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| 312 |           cin >> config::VectorPlane;
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| 313 |           break;
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| 314 |         case 'O': // VectorCut
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| 315 |           cout << Verbose(0) << "Old: " << config::VectorCut << "\t new: ";
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| 316 |           cin >> config::VectorCut;
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| 317 |           break;
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| 318 |         case 'P': // UseAddGramSch
 | 
|---|
| 319 |           cout << Verbose(0) << "Old: " << config::UseAddGramSch << "\t new: ";
 | 
|---|
| 320 |           cin >> config::UseAddGramSch;
 | 
|---|
| 321 |           break;
 | 
|---|
| 322 |         case 'Q': // Seed
 | 
|---|
| 323 |           cout << Verbose(0) << "Old: " << config::Seed << "\t new: ";
 | 
|---|
| 324 |           cin >> config::Seed;
 | 
|---|
| 325 |           break;
 | 
|---|
| 326 | 
 | 
|---|
| 327 |         case 'R': // MaxOuterStep
 | 
|---|
| 328 |           cout << Verbose(0) << "Old: " << config::MaxOuterStep << "\t new: ";
 | 
|---|
| 329 |           cin >> config::MaxOuterStep;
 | 
|---|
| 330 |           break;
 | 
|---|
| 331 |         case 'T': // OutVisStep
 | 
|---|
| 332 |           cout << Verbose(0) << "Old: " << config::OutVisStep << "\t new: ";
 | 
|---|
| 333 |           cin >> config::OutVisStep;
 | 
|---|
| 334 |           break;
 | 
|---|
| 335 |         case 'U': // OutSrcStep
 | 
|---|
| 336 |           cout << Verbose(0) << "Old: " << config::OutSrcStep << "\t new: ";
 | 
|---|
| 337 |           cin >> config::OutSrcStep;
 | 
|---|
| 338 |           break;
 | 
|---|
| 339 |         case 'X': // MaxPsiStep
 | 
|---|
| 340 |           cout << Verbose(0) << "Old: " << config::MaxPsiStep << "\t new: ";
 | 
|---|
| 341 |           cin >> config::MaxPsiStep;
 | 
|---|
| 342 |           break;
 | 
|---|
| 343 |         case 'Y': // EpsWannier
 | 
|---|
| 344 |           cout << Verbose(0) << "Old: " << config::EpsWannier << "\t new: ";
 | 
|---|
| 345 |           cin >> config::EpsWannier;
 | 
|---|
| 346 |           break;
 | 
|---|
| 347 | 
 | 
|---|
| 348 |         case 'Z': // MaxMinStep
 | 
|---|
| 349 |           cout << Verbose(0) << "Old: " << config::MaxMinStep << "\t new: ";
 | 
|---|
| 350 |           cin >> config::MaxMinStep;
 | 
|---|
| 351 |           break;
 | 
|---|
| 352 |         case 'a': // RelEpsTotalEnergy
 | 
|---|
| 353 |           cout << Verbose(0) << "Old: " << config::RelEpsTotalEnergy << "\t new: ";
 | 
|---|
| 354 |           cin >> config::RelEpsTotalEnergy;
 | 
|---|
| 355 |           break;
 | 
|---|
| 356 |         case 'b': // RelEpsKineticEnergy
 | 
|---|
| 357 |           cout << Verbose(0) << "Old: " << config::RelEpsKineticEnergy << "\t new: ";
 | 
|---|
| 358 |           cin >> config::RelEpsKineticEnergy;
 | 
|---|
| 359 |           break;
 | 
|---|
| 360 |         case 'c': // MaxMinStopStep
 | 
|---|
| 361 |           cout << Verbose(0) << "Old: " << config::MaxMinStopStep << "\t new: ";
 | 
|---|
| 362 |           cin >> config::MaxMinStopStep;
 | 
|---|
| 363 |           break;
 | 
|---|
| 364 |         case 'e': // MaxInitMinStep
 | 
|---|
| 365 |           cout << Verbose(0) << "Old: " << config::MaxInitMinStep << "\t new: ";
 | 
|---|
| 366 |           cin >> config::MaxInitMinStep;
 | 
|---|
| 367 |           break;
 | 
|---|
| 368 |         case 'f': // InitRelEpsTotalEnergy
 | 
|---|
| 369 |           cout << Verbose(0) << "Old: " << config::InitRelEpsTotalEnergy << "\t new: ";
 | 
|---|
| 370 |           cin >> config::InitRelEpsTotalEnergy;
 | 
|---|
| 371 |           break;
 | 
|---|
| 372 |         case 'g': // InitRelEpsKineticEnergy
 | 
|---|
| 373 |           cout << Verbose(0) << "Old: " << config::InitRelEpsKineticEnergy << "\t new: ";
 | 
|---|
| 374 |           cin >> config::InitRelEpsKineticEnergy;
 | 
|---|
| 375 |           break;
 | 
|---|
| 376 |         case 'h': // InitMaxMinStopStep
 | 
|---|
| 377 |           cout << Verbose(0) << "Old: " << config::InitMaxMinStopStep << "\t new: ";
 | 
|---|
| 378 |           cin >> config::InitMaxMinStopStep;
 | 
|---|
| 379 |           break;
 | 
|---|
| 380 |         
 | 
|---|
| 381 |         case 'j': // BoxLength
 | 
|---|
| 382 |           cout << Verbose(0) << "enter lower triadiagonalo form of basis matrix" << endl << endl;
 | 
|---|
| 383 |           for (int i=0;i<6;i++) {
 | 
|---|
| 384 |             cout << Verbose(0) << "Cell size" << i << ": ";
 | 
|---|
| 385 |             cin >> mol->cell_size[i];
 | 
|---|
| 386 |           }
 | 
|---|
| 387 |           break;
 | 
|---|
| 388 |         
 | 
|---|
| 389 |         case 'k': // ECut
 | 
|---|
| 390 |           cout << Verbose(0) << "Old: " << config::ECut << "\t new: ";
 | 
|---|
| 391 |           cin >> config::ECut;
 | 
|---|
| 392 |           break;
 | 
|---|
| 393 |         case 'l': // MaxLevel
 | 
|---|
| 394 |           cout << Verbose(0) << "Old: " << config::MaxLevel << "\t new: ";
 | 
|---|
| 395 |           cin >> config::MaxLevel;
 | 
|---|
| 396 |           break;
 | 
|---|
| 397 |         case 'm': // RiemannTensor
 | 
|---|
| 398 |           cout << Verbose(0) << "Old: " << config::RiemannTensor << "\t new: ";
 | 
|---|
| 399 |           cin >> config::RiemannTensor;
 | 
|---|
| 400 |           break;
 | 
|---|
| 401 |         case 'n': // LevRFactor
 | 
|---|
| 402 |           cout << Verbose(0) << "Old: " << config::LevRFactor << "\t new: ";
 | 
|---|
| 403 |           cin >> config::LevRFactor;
 | 
|---|
| 404 |           break;
 | 
|---|
| 405 |         case 'o': // RiemannLevel
 | 
|---|
| 406 |           cout << Verbose(0) << "Old: " << config::RiemannLevel << "\t new: ";
 | 
|---|
| 407 |           cin >> config::RiemannLevel;
 | 
|---|
| 408 |           break;
 | 
|---|
| 409 |         case 'p': // Lev0Factor
 | 
|---|
| 410 |           cout << Verbose(0) << "Old: " << config::Lev0Factor << "\t new: ";
 | 
|---|
| 411 |           cin >> config::Lev0Factor;
 | 
|---|
| 412 |           break;
 | 
|---|
| 413 |         case 'r': // RTActualUse
 | 
|---|
| 414 |           cout << Verbose(0) << "Old: " << config::RTActualUse << "\t new: ";
 | 
|---|
| 415 |           cin >> config::RTActualUse;
 | 
|---|
| 416 |           break;
 | 
|---|
| 417 |         case 's': // PsiType
 | 
|---|
| 418 |           cout << Verbose(0) << "Old: " << config::PsiType << "\t new: ";
 | 
|---|
| 419 |           cin >> config::PsiType;
 | 
|---|
| 420 |           break;
 | 
|---|
| 421 |         case 't': // MaxPsiDouble
 | 
|---|
| 422 |           cout << Verbose(0) << "Old: " << config::MaxPsiDouble << "\t new: ";
 | 
|---|
| 423 |           cin >> config::MaxPsiDouble;
 | 
|---|
| 424 |           break;
 | 
|---|
| 425 |         case 'u': // PsiMaxNoUp
 | 
|---|
| 426 |           cout << Verbose(0) << "Old: " << config::PsiMaxNoUp << "\t new: ";
 | 
|---|
| 427 |           cin >> config::PsiMaxNoUp;
 | 
|---|
| 428 |           break;
 | 
|---|
| 429 |         case 'v': // PsiMaxNoDown
 | 
|---|
| 430 |           cout << Verbose(0) << "Old: " << config::PsiMaxNoDown << "\t new: ";
 | 
|---|
| 431 |           cin >> config::PsiMaxNoDown;
 | 
|---|
| 432 |           break;
 | 
|---|
| 433 |         case 'w': // AddPsis
 | 
|---|
| 434 |           cout << Verbose(0) << "Old: " << config::AddPsis << "\t new: ";
 | 
|---|
| 435 |           cin >> config::AddPsis;
 | 
|---|
| 436 |           break;
 | 
|---|
| 437 | 
 | 
|---|
| 438 |         case 'x': // RCut
 | 
|---|
| 439 |           cout << Verbose(0) << "Old: " << config::RCut << "\t new: ";
 | 
|---|
| 440 |           cin >> config::RCut;
 | 
|---|
| 441 |           break;
 | 
|---|
| 442 |         case 'y': // StructOpt
 | 
|---|
| 443 |           cout << Verbose(0) << "Old: " << config::StructOpt << "\t new: ";
 | 
|---|
| 444 |           cin >> config::StructOpt;
 | 
|---|
| 445 |           break;
 | 
|---|
| 446 |         case 'z': // IsAngstroem
 | 
|---|
| 447 |           cout << Verbose(0) << "Old: " << config::IsAngstroem << "\t new: ";
 | 
|---|
| 448 |           cin >> config::IsAngstroem;
 | 
|---|
| 449 |           break;
 | 
|---|
| 450 |         case 'i': // RelativeCoord
 | 
|---|
| 451 |           cout << Verbose(0) << "Old: " << config::RelativeCoord << "\t new: ";
 | 
|---|
| 452 |           cin >> config::RelativeCoord;
 | 
|---|
| 453 |           break;
 | 
|---|
| 454 |     };
 | 
|---|
| 455 |   } while (choice != 'q');
 | 
|---|
| 456 | };
 | 
|---|
| 457 | 
 | 
|---|
| 458 | /** Tests whether a given configuration file adhears to old or new syntax.
 | 
|---|
| 459 |  * \param *filename filename of config file to be tested
 | 
|---|
| 460 |  * \param *periode pointer to a periodentafel class with all elements
 | 
|---|
| 461 |  * \param *mol pointer to molecule containing all atoms of the molecule
 | 
|---|
| 462 |  * \return 0 - old syntax, 1 - new syntax, -1 - unknown syntax 
 | 
|---|
| 463 |  */
 | 
|---|
| 464 | int config::TestSyntax(char *filename, periodentafel *periode, molecule *mol)
 | 
|---|
| 465 | {
 | 
|---|
| 466 |   int test;
 | 
|---|
| 467 |   ifstream file(filename);
 | 
|---|
| 468 |   
 | 
|---|
| 469 |   // search file for keyword: ProcPEGamma (new syntax)
 | 
|---|
| 470 |   if (ParseForParameter(1,&file,"ProcPEGamma", 0, 1, 1, int_type, &test, 1, optional)) {
 | 
|---|
| 471 |     file.close();
 | 
|---|
| 472 |     return 1;
 | 
|---|
| 473 |   }
 | 
|---|
| 474 |   // search file for keyword: ProcsGammaPsi (old syntax)
 | 
|---|
| 475 |   if (ParseForParameter(1,&file,"ProcsGammaPsi", 0, 1, 1, int_type, &test, 1, optional)) {
 | 
|---|
| 476 |     file.close();
 | 
|---|
| 477 |     return 0;
 | 
|---|
| 478 |   }
 | 
|---|
| 479 |   file.close();
 | 
|---|
| 480 |   return -1;
 | 
|---|
| 481 | }
 | 
|---|
| 482 | 
 | 
|---|
| 483 | /** Returns private config::IsAngstroem.
 | 
|---|
| 484 |  * \return IsAngstroem
 | 
|---|
| 485 |  */
 | 
|---|
| 486 | bool config::GetIsAngstroem() const
 | 
|---|
| 487 | {
 | 
|---|
| 488 |   return (IsAngstroem == 1);
 | 
|---|
| 489 | };
 | 
|---|
| 490 | 
 | 
|---|
| 491 | /** Returns private config::*defaultpath.
 | 
|---|
| 492 |  * \return *defaultpath
 | 
|---|
| 493 |  */
 | 
|---|
| 494 | char * config::GetDefaultPath() const
 | 
|---|
| 495 | {
 | 
|---|
| 496 |   return defaultpath;
 | 
|---|
| 497 | };
 | 
|---|
| 498 | 
 | 
|---|
| 499 | 
 | 
|---|
| 500 | /** Returns private config::*defaultpath.
 | 
|---|
| 501 |  * \return *defaultpath
 | 
|---|
| 502 |  */
 | 
|---|
| 503 | void config::SetDefaultPath(const char *path)
 | 
|---|
| 504 | {
 | 
|---|
| 505 |   strcpy(defaultpath, path);
 | 
|---|
| 506 | };
 | 
|---|
| 507 | 
 | 
|---|
| 508 | /** Retrieves the path in the given config file name.
 | 
|---|
| 509 |  * \param filename config file string
 | 
|---|
| 510 |  */
 | 
|---|
| 511 | void config::RetrieveConfigPathAndName(string filename)
 | 
|---|
| 512 | {
 | 
|---|
| 513 |   char *ptr = NULL;
 | 
|---|
| 514 |   char *buffer = new char[MAXSTRINGSIZE];
 | 
|---|
| 515 |   strncpy(buffer, filename.c_str(), MAXSTRINGSIZE);
 | 
|---|
| 516 |   int last = -1;
 | 
|---|
| 517 |   for(last=MAXSTRINGSIZE;last--;) {
 | 
|---|
| 518 |     if (buffer[last] == '/')
 | 
|---|
| 519 |       break;
 | 
|---|
| 520 |   }
 | 
|---|
| 521 |   if (last == -1) { // no path in front, set to local directory.
 | 
|---|
| 522 |     strcpy(configpath, "./");
 | 
|---|
| 523 |     ptr = buffer;
 | 
|---|
| 524 |   } else {
 | 
|---|
| 525 |     strncpy(configpath, buffer, last+1);
 | 
|---|
| 526 |     ptr = &buffer[last+1];
 | 
|---|
| 527 |     if (last < 254)
 | 
|---|
| 528 |       configpath[last+1]='\0';
 | 
|---|
| 529 |   }
 | 
|---|
| 530 |   strcpy(configname, ptr);
 | 
|---|
| 531 |   cout << "Found configpath: " << configpath << ", dir slash was found at " << last << ", config name is " << configname << "." << endl;
 | 
|---|
| 532 |   delete[](buffer);
 | 
|---|
| 533 | };
 | 
|---|
| 534 | 
 | 
|---|
| 535 | 
 | 
|---|
| 536 | /** Initializes config file structure by loading elements from a give file.
 | 
|---|
| 537 |  * \param *file input file stream being the opened config file
 | 
|---|
| 538 |  * \param *periode pointer to a periodentafel class with all elements
 | 
|---|
| 539 |  * \param *mol pointer to molecule containing all atoms of the molecule 
 | 
|---|
| 540 |  */
 | 
|---|
| 541 | void config::Load(char *filename, periodentafel *periode, molecule *mol)
 | 
|---|
| 542 | {
 | 
|---|
| 543 |   ifstream *file = new ifstream(filename);
 | 
|---|
| 544 |   if (file == NULL) {
 | 
|---|
| 545 |     cerr << "ERROR: config file " << filename << " missing!" << endl;
 | 
|---|
| 546 |     return;
 | 
|---|
| 547 |   }
 | 
|---|
| 548 |   RetrieveConfigPathAndName(filename);
 | 
|---|
| 549 |   // ParseParameters
 | 
|---|
| 550 |   
 | 
|---|
| 551 |   /* Oeffne Hauptparameterdatei */
 | 
|---|
| 552 |   int di;
 | 
|---|
| 553 |   double BoxLength[9];
 | 
|---|
| 554 |   string zeile;
 | 
|---|
| 555 |   string dummy;
 | 
|---|
| 556 |   element *elementhash[MAX_ELEMENTS];
 | 
|---|
| 557 |   char name[MAX_ELEMENTS];
 | 
|---|
| 558 |   char keyword[MAX_ELEMENTS];
 | 
|---|
| 559 |   int Z, No[MAX_ELEMENTS];
 | 
|---|
| 560 |   int verbose = 0;
 | 
|---|
| 561 |   double value[3];
 | 
|---|
| 562 |   
 | 
|---|
| 563 |   InitThermostats(file);
 | 
|---|
| 564 |   
 | 
|---|
| 565 |   /* Namen einlesen */
 | 
|---|
| 566 | 
 | 
|---|
| 567 |   ParseForParameter(verbose,file, "mainname", 0, 1, 1, string_type, (config::mainname), 1, critical);
 | 
|---|
| 568 |   ParseForParameter(verbose,file, "defaultpath", 0, 1, 1, string_type, (config::defaultpath), 1, critical);
 | 
|---|
| 569 |   ParseForParameter(verbose,file, "pseudopotpath", 0, 1, 1, string_type, (config::pseudopotpath), 1, critical);
 | 
|---|
| 570 |   ParseForParameter(verbose,file,"ProcPEGamma", 0, 1, 1, int_type, &(config::ProcPEGamma), 1, critical);
 | 
|---|
| 571 |   ParseForParameter(verbose,file,"ProcPEPsi", 0, 1, 1, int_type, &(config::ProcPEPsi), 1, critical);
 | 
|---|
| 572 | 
 | 
|---|
| 573 |   if (!ParseForParameter(verbose,file,"Seed", 0, 1, 1, int_type, &(config::Seed), 1, optional))
 | 
|---|
| 574 |     config::Seed = 1;
 | 
|---|
| 575 | 
 | 
|---|
| 576 |   if(!ParseForParameter(verbose,file,"DoOutOrbitals", 0, 1, 1, int_type, &(config::DoOutOrbitals), 1, optional)) {
 | 
|---|
| 577 |     config::DoOutOrbitals = 0;
 | 
|---|
| 578 |   } else {
 | 
|---|
| 579 |     if (config::DoOutOrbitals < 0) config::DoOutOrbitals = 0;
 | 
|---|
| 580 |     if (config::DoOutOrbitals > 1) config::DoOutOrbitals = 1;
 | 
|---|
| 581 |   }
 | 
|---|
| 582 |   ParseForParameter(verbose,file,"DoOutVis", 0, 1, 1, int_type, &(config::DoOutVis), 1, critical);
 | 
|---|
| 583 |   if (config::DoOutVis < 0) config::DoOutVis = 0;
 | 
|---|
| 584 |   if (config::DoOutVis > 1) config::DoOutVis = 1;
 | 
|---|
| 585 |   if (!ParseForParameter(verbose,file,"VectorPlane", 0, 1, 1, int_type, &(config::VectorPlane), 1, optional))
 | 
|---|
| 586 |     config::VectorPlane = -1;
 | 
|---|
| 587 |   if (!ParseForParameter(verbose,file,"VectorCut", 0, 1, 1, double_type, &(config::VectorCut), 1, optional))
 | 
|---|
| 588 |     config::VectorCut = 0.;
 | 
|---|
| 589 |   ParseForParameter(verbose,file,"DoOutMes", 0, 1, 1, int_type, &(config::DoOutMes), 1, critical);
 | 
|---|
| 590 |   if (config::DoOutMes < 0) config::DoOutMes = 0;
 | 
|---|
| 591 |   if (config::DoOutMes > 1) config::DoOutMes = 1;
 | 
|---|
| 592 |   if (!ParseForParameter(verbose,file,"DoOutCurr", 0, 1, 1, int_type, &(config::DoOutCurrent), 1, optional))
 | 
|---|
| 593 |     config::DoOutCurrent = 0;
 | 
|---|
| 594 |   if (config::DoOutCurrent < 0) config::DoOutCurrent = 0;
 | 
|---|
| 595 |   if (config::DoOutCurrent > 1) config::DoOutCurrent = 1; 
 | 
|---|
| 596 |   ParseForParameter(verbose,file,"AddGramSch", 0, 1, 1, int_type, &(config::UseAddGramSch), 1, critical);
 | 
|---|
| 597 |   if (config::UseAddGramSch < 0) config::UseAddGramSch = 0;
 | 
|---|
| 598 |   if (config::UseAddGramSch > 2) config::UseAddGramSch = 2;
 | 
|---|
| 599 |   if(!ParseForParameter(verbose,file,"DoWannier", 0, 1, 1, int_type, &(config::DoWannier), 1, optional)) {
 | 
|---|
| 600 |     config::DoWannier = 0;
 | 
|---|
| 601 |   } else {
 | 
|---|
| 602 |     if (config::DoWannier < 0) config::DoWannier = 0;
 | 
|---|
| 603 |     if (config::DoWannier > 1) config::DoWannier = 1;
 | 
|---|
| 604 |   }
 | 
|---|
| 605 |   if(!ParseForParameter(verbose,file,"CommonWannier", 0, 1, 1, int_type, &(config::CommonWannier), 1, optional)) {
 | 
|---|
| 606 |     config::CommonWannier = 0;
 | 
|---|
| 607 |   } else {
 | 
|---|
| 608 |     if (config::CommonWannier < 0) config::CommonWannier = 0;
 | 
|---|
| 609 |     if (config::CommonWannier > 4) config::CommonWannier = 4;
 | 
|---|
| 610 |   }
 | 
|---|
| 611 |   if(!ParseForParameter(verbose,file,"SawtoothStart", 0, 1, 1, double_type, &(config::SawtoothStart), 1, optional)) {
 | 
|---|
| 612 |     config::SawtoothStart = 0.01;
 | 
|---|
| 613 |   } else {
 | 
|---|
| 614 |     if (config::SawtoothStart < 0.) config::SawtoothStart = 0.;
 | 
|---|
| 615 |     if (config::SawtoothStart > 1.) config::SawtoothStart = 1.;
 | 
|---|
| 616 |   }
 | 
|---|
| 617 |   
 | 
|---|
| 618 |   if (ParseForParameter(verbose,file,"DoConstrainedMD", 0, 1, 1, int_type, &(config::DoConstrainedMD), 1, optional))
 | 
|---|
| 619 |     if (config::DoConstrainedMD < 0) 
 | 
|---|
| 620 |       config::DoConstrainedMD = 0;
 | 
|---|
| 621 |   ParseForParameter(verbose,file,"MaxOuterStep", 0, 1, 1, int_type, &(config::MaxOuterStep), 1, critical);
 | 
|---|
| 622 |   if (!ParseForParameter(verbose,file,"Deltat", 0, 1, 1, double_type, &(config::Deltat), 1, optional))
 | 
|---|
| 623 |     config::Deltat = 1;
 | 
|---|
| 624 |   ParseForParameter(verbose,file,"OutVisStep", 0, 1, 1, int_type, &(config::OutVisStep), 1, optional);
 | 
|---|
| 625 |   ParseForParameter(verbose,file,"OutSrcStep", 0, 1, 1, int_type, &(config::OutSrcStep), 1, optional);
 | 
|---|
| 626 |   ParseForParameter(verbose,file,"TargetTemp", 0, 1, 1, double_type, &(config::TargetTemp), 1, optional);
 | 
|---|
| 627 |   //ParseForParameter(verbose,file,"Thermostat", 0, 1, 1, int_type, &(config::ScaleTempStep), 1, optional);
 | 
|---|
| 628 |   if (!ParseForParameter(verbose,file,"EpsWannier", 0, 1, 1, double_type, &(config::EpsWannier), 1, optional))
 | 
|---|
| 629 |     config::EpsWannier = 1e-8;
 | 
|---|
| 630 |   
 | 
|---|
| 631 |   // stop conditions
 | 
|---|
| 632 |   //if (config::MaxOuterStep <= 0) config::MaxOuterStep = 1;
 | 
|---|
| 633 |   ParseForParameter(verbose,file,"MaxPsiStep", 0, 1, 1, int_type, &(config::MaxPsiStep), 1, critical);
 | 
|---|
| 634 |   if (config::MaxPsiStep <= 0) config::MaxPsiStep = 3;
 | 
|---|
| 635 |   
 | 
|---|
| 636 |   ParseForParameter(verbose,file,"MaxMinStep", 0, 1, 1, int_type, &(config::MaxMinStep), 1, critical);
 | 
|---|
| 637 |   ParseForParameter(verbose,file,"RelEpsTotalE", 0, 1, 1, double_type, &(config::RelEpsTotalEnergy), 1, critical);
 | 
|---|
| 638 |   ParseForParameter(verbose,file,"RelEpsKineticE", 0, 1, 1, double_type, &(config::RelEpsKineticEnergy), 1, critical);
 | 
|---|
| 639 |   ParseForParameter(verbose,file,"MaxMinStopStep", 0, 1, 1, int_type, &(config::MaxMinStopStep), 1, critical);
 | 
|---|
| 640 |   ParseForParameter(verbose,file,"MaxMinGapStopStep", 0, 1, 1, int_type, &(config::MaxMinGapStopStep), 1, critical);
 | 
|---|
| 641 |   if (config::MaxMinStep <= 0) config::MaxMinStep = config::MaxPsiStep;
 | 
|---|
| 642 |   if (config::MaxMinStopStep < 1) config::MaxMinStopStep = 1;
 | 
|---|
| 643 |   if (config::MaxMinGapStopStep < 1) config::MaxMinGapStopStep = 1;
 | 
|---|
| 644 |   
 | 
|---|
| 645 |   ParseForParameter(verbose,file,"MaxInitMinStep", 0, 1, 1, int_type, &(config::MaxInitMinStep), 1, critical);
 | 
|---|
| 646 |   ParseForParameter(verbose,file,"InitRelEpsTotalE", 0, 1, 1, double_type, &(config::InitRelEpsTotalEnergy), 1, critical);
 | 
|---|
| 647 |   ParseForParameter(verbose,file,"InitRelEpsKineticE", 0, 1, 1, double_type, &(config::InitRelEpsKineticEnergy), 1, critical);
 | 
|---|
| 648 |   ParseForParameter(verbose,file,"InitMaxMinStopStep", 0, 1, 1, int_type, &(config::InitMaxMinStopStep), 1, critical);
 | 
|---|
| 649 |   ParseForParameter(verbose,file,"InitMaxMinGapStopStep", 0, 1, 1, int_type, &(config::InitMaxMinGapStopStep), 1, critical);
 | 
|---|
| 650 |   if (config::MaxInitMinStep <= 0) config::MaxInitMinStep = config::MaxPsiStep;
 | 
|---|
| 651 |   if (config::InitMaxMinStopStep < 1) config::InitMaxMinStopStep = 1;
 | 
|---|
| 652 |   if (config::InitMaxMinGapStopStep < 1) config::InitMaxMinGapStopStep = 1;
 | 
|---|
| 653 |   
 | 
|---|
| 654 |   // Unit cell and magnetic field
 | 
|---|
| 655 |   ParseForParameter(verbose,file, "BoxLength", 0, 3, 3, lower_trigrid, BoxLength, 1, critical); /* Lattice->RealBasis */
 | 
|---|
| 656 |   mol->cell_size[0] = BoxLength[0];
 | 
|---|
| 657 |   mol->cell_size[1] = BoxLength[3];
 | 
|---|
| 658 |   mol->cell_size[2] = BoxLength[4];
 | 
|---|
| 659 |   mol->cell_size[3] = BoxLength[6];
 | 
|---|
| 660 |   mol->cell_size[4] = BoxLength[7];
 | 
|---|
| 661 |   mol->cell_size[5] = BoxLength[8];
 | 
|---|
| 662 |   if (1) fprintf(stderr,"\n");
 | 
|---|
| 663 | 
 | 
|---|
| 664 |   ParseForParameter(verbose,file,"DoPerturbation", 0, 1, 1, int_type, &(config::DoPerturbation), 1, optional);
 | 
|---|
| 665 |   ParseForParameter(verbose,file,"DoOutNICS", 0, 1, 1, int_type, &(config::DoOutNICS), 1, optional);
 | 
|---|
| 666 |   if (!ParseForParameter(verbose,file,"DoFullCurrent", 0, 1, 1, int_type, &(config::DoFullCurrent), 1, optional))
 | 
|---|
| 667 |     config::DoFullCurrent = 0;
 | 
|---|
| 668 |   if (config::DoFullCurrent < 0) config::DoFullCurrent = 0;
 | 
|---|
| 669 |   if (config::DoFullCurrent > 2) config::DoFullCurrent = 2; 
 | 
|---|
| 670 |   if (config::DoOutNICS < 0) config::DoOutNICS = 0;
 | 
|---|
| 671 |   if (config::DoOutNICS > 2) config::DoOutNICS = 2; 
 | 
|---|
| 672 |   if (config::DoPerturbation == 0) {
 | 
|---|
| 673 |     config::DoFullCurrent = 0;
 | 
|---|
| 674 |     config::DoOutNICS = 0;
 | 
|---|
| 675 |   }
 | 
|---|
| 676 | 
 | 
|---|
| 677 |   ParseForParameter(verbose,file,"ECut", 0, 1, 1, double_type, &(config::ECut), 1, critical);
 | 
|---|
| 678 |   ParseForParameter(verbose,file,"MaxLevel", 0, 1, 1, int_type, &(config::MaxLevel), 1, critical);
 | 
|---|
| 679 |   ParseForParameter(verbose,file,"Level0Factor", 0, 1, 1, int_type, &(config::Lev0Factor), 1, critical);
 | 
|---|
| 680 |   if (config::Lev0Factor < 2) {
 | 
|---|
| 681 |     config::Lev0Factor = 2;
 | 
|---|
| 682 |   }
 | 
|---|
| 683 |   ParseForParameter(verbose,file,"RiemannTensor", 0, 1, 1, int_type, &di, 1, critical);
 | 
|---|
| 684 |   if (di >= 0 && di < 2) {
 | 
|---|
| 685 |     config::RiemannTensor = di;
 | 
|---|
| 686 |   } else {
 | 
|---|
| 687 |     fprintf(stderr, "0 <= RiemanTensor < 2: 0 UseNotRT, 1 UseRT");
 | 
|---|
| 688 |     exit(1); 
 | 
|---|
| 689 |   }
 | 
|---|
| 690 |   switch (config::RiemannTensor) {
 | 
|---|
| 691 |     case 0: //UseNoRT
 | 
|---|
| 692 |       if (config::MaxLevel < 2) {
 | 
|---|
| 693 |         config::MaxLevel = 2;
 | 
|---|
| 694 |       }
 | 
|---|
| 695 |       config::LevRFactor = 2;
 | 
|---|
| 696 |       config::RTActualUse = 0;
 | 
|---|
| 697 |       break;
 | 
|---|
| 698 |     case 1: // UseRT
 | 
|---|
| 699 |       if (config::MaxLevel < 3) {
 | 
|---|
| 700 |         config::MaxLevel = 3;
 | 
|---|
| 701 |       }
 | 
|---|
| 702 |       ParseForParameter(verbose,file,"RiemannLevel", 0, 1, 1, int_type, &(config::RiemannLevel), 1, critical);
 | 
|---|
| 703 |       if (config::RiemannLevel < 2) {
 | 
|---|
| 704 |         config::RiemannLevel = 2;
 | 
|---|
| 705 |       } 
 | 
|---|
| 706 |       if (config::RiemannLevel > config::MaxLevel-1) {
 | 
|---|
| 707 |         config::RiemannLevel = config::MaxLevel-1;
 | 
|---|
| 708 |       }
 | 
|---|
| 709 |       ParseForParameter(verbose,file,"LevRFactor", 0, 1, 1, int_type, &(config::LevRFactor), 1, critical);
 | 
|---|
| 710 |       if (config::LevRFactor < 2) {
 | 
|---|
| 711 |         config::LevRFactor = 2;
 | 
|---|
| 712 |       } 
 | 
|---|
| 713 |       config::Lev0Factor = 2;
 | 
|---|
| 714 |       config::RTActualUse = 2;
 | 
|---|
| 715 |       break;
 | 
|---|
| 716 |   }
 | 
|---|
| 717 |   ParseForParameter(verbose,file,"PsiType", 0, 1, 1, int_type, &di, 1, critical);
 | 
|---|
| 718 |   if (di >= 0 && di < 2) {
 | 
|---|
| 719 |     config::PsiType = di;
 | 
|---|
| 720 |   } else {
 | 
|---|
| 721 |     fprintf(stderr, "0 <= PsiType < 2: 0 UseSpinDouble, 1 UseSpinUpDown");
 | 
|---|
| 722 |     exit(1); 
 | 
|---|
| 723 |   }
 | 
|---|
| 724 |   switch (config::PsiType) {
 | 
|---|
| 725 |   case 0: // SpinDouble
 | 
|---|
| 726 |     ParseForParameter(verbose,file,"MaxPsiDouble", 0, 1, 1, int_type, &(config::MaxPsiDouble), 1, critical);
 | 
|---|
| 727 |     ParseForParameter(verbose,file,"AddPsis", 0, 1, 1, int_type, &(config::AddPsis), 1, optional);
 | 
|---|
| 728 |     break;
 | 
|---|
| 729 |   case 1: // SpinUpDown
 | 
|---|
| 730 |     if (config::ProcPEGamma % 2) config::ProcPEGamma*=2;
 | 
|---|
| 731 |     ParseForParameter(verbose,file,"PsiMaxNoUp", 0, 1, 1, int_type, &(config::PsiMaxNoUp), 1, critical);
 | 
|---|
| 732 |     ParseForParameter(verbose,file,"PsiMaxNoDown", 0, 1, 1, int_type, &(config::PsiMaxNoDown), 1, critical);
 | 
|---|
| 733 |     ParseForParameter(verbose,file,"AddPsis", 0, 1, 1, int_type, &(config::AddPsis), 1, optional);
 | 
|---|
| 734 |     break;
 | 
|---|
| 735 |   }
 | 
|---|
| 736 |   
 | 
|---|
| 737 |   // IonsInitRead
 | 
|---|
| 738 |   
 | 
|---|
| 739 |   ParseForParameter(verbose,file,"RCut", 0, 1, 1, double_type, &(config::RCut), 1, critical);
 | 
|---|
| 740 |   ParseForParameter(verbose,file,"IsAngstroem", 0, 1, 1, int_type, &(config::IsAngstroem), 1, critical);
 | 
|---|
| 741 |   ParseForParameter(verbose,file,"MaxTypes", 0, 1, 1, int_type, &(config::MaxTypes), 1, critical);
 | 
|---|
| 742 |   if (!ParseForParameter(verbose,file,"RelativeCoord", 0, 1, 1, int_type, &(config::RelativeCoord) , 1, optional))
 | 
|---|
| 743 |     config::RelativeCoord = 0;
 | 
|---|
| 744 |   if (!ParseForParameter(verbose,file,"StructOpt", 0, 1, 1, int_type, &(config::StructOpt), 1, optional))
 | 
|---|
| 745 |     config::StructOpt = 0;
 | 
|---|
| 746 |   if (MaxTypes == 0) {
 | 
|---|
| 747 |     cerr << "There are no atoms according to MaxTypes in this config file." << endl;
 | 
|---|
| 748 |   } else {
 | 
|---|
| 749 |     // prescan number of ions per type
 | 
|---|
| 750 |     cout << Verbose(0) << "Prescanning ions per type: " << endl;
 | 
|---|
| 751 |     for (int i=0; i < config::MaxTypes; i++) {
 | 
|---|
| 752 |       sprintf(name,"Ion_Type%i",i+1);
 | 
|---|
| 753 |       ParseForParameter(verbose,file, (const char*)name, 0, 1, 1, int_type, &No[i], 1, critical);
 | 
|---|
| 754 |       ParseForParameter(verbose,file, name, 0, 2, 1, int_type, &Z, 1, critical);
 | 
|---|
| 755 |       elementhash[i] = periode->FindElement(Z);
 | 
|---|
| 756 |       cout << Verbose(1) << i << ". Z = " << elementhash[i]->Z << " with " << No[i] << " ions." << endl; 
 | 
|---|
| 757 |     }
 | 
|---|
| 758 |     int repetition = 0; // which repeated keyword shall be read
 | 
|---|
| 759 |   
 | 
|---|
| 760 |     map<int, atom *> AtomList[config::MaxTypes];
 | 
|---|
| 761 |     if (!FastParsing) {
 | 
|---|
| 762 |       // parse in trajectories
 | 
|---|
| 763 |       bool status = true;
 | 
|---|
| 764 |       atom *neues = NULL;
 | 
|---|
| 765 |       while (status) {
 | 
|---|
| 766 |         cout << "Currently parsing MD step " << repetition << "." << endl;
 | 
|---|
| 767 |         for (int i=0; i < config::MaxTypes; i++) {
 | 
|---|
| 768 |           sprintf(name,"Ion_Type%i",i+1);
 | 
|---|
| 769 |           for(int j=0;j<No[i];j++) {
 | 
|---|
| 770 |             sprintf(keyword,"%s_%i",name, j+1);
 | 
|---|
| 771 |             if (repetition == 0) {
 | 
|---|
| 772 |               neues = new atom();
 | 
|---|
| 773 |               AtomList[i][j] = neues;
 | 
|---|
| 774 |               neues->type = elementhash[i]; // find element type
 | 
|---|
| 775 |               mol->AddAtom(neues);
 | 
|---|
| 776 |             } else
 | 
|---|
| 777 |               neues = AtomList[i][j];
 | 
|---|
| 778 |             status = (status && 
 | 
|---|
| 779 |                     ParseForParameter(verbose,file, keyword, 0, 1, 1, double_type, &neues->x.x[0], 1, (repetition == 0) ? critical : optional) &&
 | 
|---|
| 780 |                     ParseForParameter(verbose,file, keyword, 0, 2, 1, double_type, &neues->x.x[1], 1, (repetition == 0) ? critical : optional) &&
 | 
|---|
| 781 |                     ParseForParameter(verbose,file, keyword, 0, 3, 1, double_type, &neues->x.x[2], 1, (repetition == 0) ? critical : optional) &&
 | 
|---|
| 782 |                     ParseForParameter(verbose,file, keyword, 0, 4, 1, int_type, &neues->FixedIon, 1, (repetition == 0) ? critical : optional));
 | 
|---|
| 783 |             if (!status) break;
 | 
|---|
| 784 |     
 | 
|---|
| 785 |             // check size of vectors
 | 
|---|
| 786 |             if (mol->Trajectories[neues].R.size() <= (unsigned int)(repetition)) {
 | 
|---|
| 787 |               //cout << "Increasing size for trajectory array of " << keyword << " to " << (repetition+10) << "." << endl;
 | 
|---|
| 788 |               mol->Trajectories[neues].R.resize(repetition+10);
 | 
|---|
| 789 |               mol->Trajectories[neues].U.resize(repetition+10);
 | 
|---|
| 790 |               mol->Trajectories[neues].F.resize(repetition+10);
 | 
|---|
| 791 |             }
 | 
|---|
| 792 |           
 | 
|---|
| 793 |             // put into trajectories list
 | 
|---|
| 794 |             for (int d=0;d<NDIM;d++)
 | 
|---|
| 795 |               mol->Trajectories[neues].R.at(repetition).x[d] = neues->x.x[d];
 | 
|---|
| 796 |             
 | 
|---|
| 797 |             // parse velocities if present
 | 
|---|
| 798 |             if(!ParseForParameter(verbose,file, keyword, 0, 5, 1, double_type, &neues->v.x[0], 1,optional))
 | 
|---|
| 799 |               neues->v.x[0] = 0.;
 | 
|---|
| 800 |             if(!ParseForParameter(verbose,file, keyword, 0, 6, 1, double_type, &neues->v.x[1], 1,optional))
 | 
|---|
| 801 |               neues->v.x[1] = 0.;
 | 
|---|
| 802 |             if(!ParseForParameter(verbose,file, keyword, 0, 7, 1, double_type, &neues->v.x[2], 1,optional))
 | 
|---|
| 803 |               neues->v.x[2] = 0.;
 | 
|---|
| 804 |             for (int d=0;d<NDIM;d++)
 | 
|---|
| 805 |               mol->Trajectories[neues].U.at(repetition).x[d] = neues->v.x[d];
 | 
|---|
| 806 |       
 | 
|---|
| 807 |             // parse forces if present
 | 
|---|
| 808 |             if(!ParseForParameter(verbose,file, keyword, 0, 8, 1, double_type, &value[0], 1,optional))
 | 
|---|
| 809 |               value[0] = 0.;
 | 
|---|
| 810 |             if(!ParseForParameter(verbose,file, keyword, 0, 9, 1, double_type, &value[1], 1,optional))
 | 
|---|
| 811 |               value[1] = 0.;
 | 
|---|
| 812 |             if(!ParseForParameter(verbose,file, keyword, 1, 10, 1, double_type, &value[2], 1,optional))
 | 
|---|
| 813 |               value[2] = 0.;
 | 
|---|
| 814 |             for (int d=0;d<NDIM;d++)
 | 
|---|
| 815 |               mol->Trajectories[neues].F.at(repetition).x[d] = value[d];
 | 
|---|
| 816 |   
 | 
|---|
| 817 |   //            cout << "Parsed position of step " << (repetition) << ": ("; 
 | 
|---|
| 818 |   //            for (int d=0;d<NDIM;d++)
 | 
|---|
| 819 |   //              cout << mol->Trajectories[neues].R.at(repetition).x[d] << " ";          // next step
 | 
|---|
| 820 |   //            cout << ")\t(";
 | 
|---|
| 821 |   //            for (int d=0;d<NDIM;d++)
 | 
|---|
| 822 |   //              cout << mol->Trajectories[neues].U.at(repetition).x[d] << " ";          // next step
 | 
|---|
| 823 |   //            cout << ")\t(";
 | 
|---|
| 824 |   //            for (int d=0;d<NDIM;d++)
 | 
|---|
| 825 |   //              cout << mol->Trajectories[neues].F.at(repetition).x[d] << " ";          // next step
 | 
|---|
| 826 |   //            cout << ")" << endl;
 | 
|---|
| 827 |           }
 | 
|---|
| 828 |         }
 | 
|---|
| 829 |         repetition++;
 | 
|---|
| 830 |       }
 | 
|---|
| 831 |       repetition--;
 | 
|---|
| 832 |       cout << "Found " << repetition << " trajectory steps." << endl;
 | 
|---|
| 833 |       mol->MDSteps = repetition;
 | 
|---|
| 834 |     } else {
 | 
|---|
| 835 |       // find the maximum number of MD steps so that we may parse last one (Ion_Type1_1 must always be present, because is the first atom)
 | 
|---|
| 836 |       repetition = 0;
 | 
|---|
| 837 |       while ( ParseForParameter(verbose,file, "Ion_Type1_1", 0, 1, 1, double_type, &value[0], repetition, (repetition == 0) ? critical : optional) &&
 | 
|---|
| 838 |               ParseForParameter(verbose,file, "Ion_Type1_1", 0, 2, 1, double_type, &value[1], repetition, (repetition == 0) ? critical : optional) &&
 | 
|---|
| 839 |               ParseForParameter(verbose,file, "Ion_Type1_1", 0, 3, 1, double_type, &value[2], repetition, (repetition == 0) ? critical : optional))
 | 
|---|
| 840 |         repetition++;
 | 
|---|
| 841 |       cout << "I found " << repetition << " times the keyword Ion_Type1_1." << endl;
 | 
|---|
| 842 |       // parse in molecule coordinates
 | 
|---|
| 843 |       for (int i=0; i < config::MaxTypes; i++) {
 | 
|---|
| 844 |         sprintf(name,"Ion_Type%i",i+1);
 | 
|---|
| 845 |         for(int j=0;j<No[i];j++) {
 | 
|---|
| 846 |           sprintf(keyword,"%s_%i",name, j+1);
 | 
|---|
| 847 |           atom *neues = new atom();
 | 
|---|
| 848 |           // then parse for each atom the coordinates as often as present
 | 
|---|
| 849 |           ParseForParameter(verbose,file, keyword, 0, 1, 1, double_type, &neues->x.x[0], repetition,critical);
 | 
|---|
| 850 |           ParseForParameter(verbose,file, keyword, 0, 2, 1, double_type, &neues->x.x[1], repetition,critical);
 | 
|---|
| 851 |           ParseForParameter(verbose,file, keyword, 0, 3, 1, double_type, &neues->x.x[2], repetition,critical);
 | 
|---|
| 852 |           ParseForParameter(verbose,file, keyword, 0, 4, 1, int_type, &neues->FixedIon, repetition,critical);
 | 
|---|
| 853 |           if(!ParseForParameter(verbose,file, keyword, 0, 5, 1, double_type, &neues->v.x[0], repetition,optional))
 | 
|---|
| 854 |             neues->v.x[0] = 0.;
 | 
|---|
| 855 |           if(!ParseForParameter(verbose,file, keyword, 0, 6, 1, double_type, &neues->v.x[1], repetition,optional))
 | 
|---|
| 856 |             neues->v.x[1] = 0.;
 | 
|---|
| 857 |           if(!ParseForParameter(verbose,file, keyword, 0, 7, 1, double_type, &neues->v.x[2], repetition,optional))
 | 
|---|
| 858 |             neues->v.x[2] = 0.;
 | 
|---|
| 859 |           // here we don't care if forces are present (last in trajectories is always equal to current position)
 | 
|---|
| 860 |           neues->type = elementhash[i]; // find element type
 | 
|---|
| 861 |           mol->AddAtom(neues);
 | 
|---|
| 862 |         }
 | 
|---|
| 863 |       }
 | 
|---|
| 864 |     }
 | 
|---|
| 865 |   }
 | 
|---|
| 866 |   file->close();
 | 
|---|
| 867 |   delete(file);
 | 
|---|
| 868 | };
 | 
|---|
| 869 | 
 | 
|---|
| 870 | /** Initializes config file structure by loading elements from a give file with old pcp syntax.
 | 
|---|
| 871 |  * \param *file input file stream being the opened config file with old pcp syntax
 | 
|---|
| 872 |  * \param *periode pointer to a periodentafel class with all elements
 | 
|---|
| 873 |  * \param *mol pointer to molecule containing all atoms of the molecule 
 | 
|---|
| 874 |  */
 | 
|---|
| 875 | void config::LoadOld(char *filename, periodentafel *periode, molecule *mol)
 | 
|---|
| 876 | {
 | 
|---|
| 877 |   ifstream *file = new ifstream(filename);
 | 
|---|
| 878 |   if (file == NULL) {
 | 
|---|
| 879 |     cerr << "ERROR: config file " << filename << " missing!" << endl;
 | 
|---|
| 880 |     return;
 | 
|---|
| 881 |   }
 | 
|---|
| 882 |   RetrieveConfigPathAndName(filename);
 | 
|---|
| 883 |   // ParseParameters
 | 
|---|
| 884 |   
 | 
|---|
| 885 |   /* Oeffne Hauptparameterdatei */
 | 
|---|
| 886 |   int l, i, di;
 | 
|---|
| 887 |   double a,b;
 | 
|---|
| 888 |   double BoxLength[9];
 | 
|---|
| 889 |   string zeile;
 | 
|---|
| 890 |   string dummy;
 | 
|---|
| 891 |   element *elementhash[128];
 | 
|---|
| 892 |   int Z, No, AtomNo, found;
 | 
|---|
| 893 |   int verbose = 0;
 | 
|---|
| 894 |   
 | 
|---|
| 895 |   /* Namen einlesen */
 | 
|---|
| 896 | 
 | 
|---|
| 897 |   ParseForParameter(verbose,file, "mainname", 0, 1, 1, string_type, (config::mainname), 1, critical);
 | 
|---|
| 898 |   ParseForParameter(verbose,file, "defaultpath", 0, 1, 1, string_type, (config::defaultpath), 1, critical);
 | 
|---|
| 899 |   ParseForParameter(verbose,file, "pseudopotpath", 0, 1, 1, string_type, (config::pseudopotpath), 1, critical);
 | 
|---|
| 900 |   ParseForParameter(verbose,file, "ProcsGammaPsi", 0, 1, 1, int_type, &(config::ProcPEGamma), 1, critical);
 | 
|---|
| 901 |   ParseForParameter(verbose,file, "ProcsGammaPsi", 0, 2, 1, int_type, &(config::ProcPEPsi), 1, critical);
 | 
|---|
| 902 |   config::Seed = 1;
 | 
|---|
| 903 |   config::DoOutOrbitals = 0;
 | 
|---|
| 904 |   ParseForParameter(verbose,file,"DoOutVis", 0, 1, 1, int_type, &(config::DoOutVis), 1, critical);
 | 
|---|
| 905 |   if (config::DoOutVis < 0) config::DoOutVis = 0;
 | 
|---|
| 906 |   if (config::DoOutVis > 1) config::DoOutVis = 1;
 | 
|---|
| 907 |   config::VectorPlane = -1;
 | 
|---|
| 908 |   config::VectorCut = 0.;
 | 
|---|
| 909 |   ParseForParameter(verbose,file,"DoOutMes", 0, 1, 1, int_type, &(config::DoOutMes), 1, critical);
 | 
|---|
| 910 |   if (config::DoOutMes < 0) config::DoOutMes = 0;
 | 
|---|
| 911 |   if (config::DoOutMes > 1) config::DoOutMes = 1;
 | 
|---|
| 912 |   config::DoOutCurrent = 0;
 | 
|---|
| 913 |   ParseForParameter(verbose,file,"AddGramSch", 0, 1, 1, int_type, &(config::UseAddGramSch), 1, critical);
 | 
|---|
| 914 |   if (config::UseAddGramSch < 0) config::UseAddGramSch = 0;
 | 
|---|
| 915 |   if (config::UseAddGramSch > 2) config::UseAddGramSch = 2;
 | 
|---|
| 916 |   config::CommonWannier = 0;
 | 
|---|
| 917 |   config::SawtoothStart = 0.01;
 | 
|---|
| 918 | 
 | 
|---|
| 919 |   ParseForParameter(verbose,file,"MaxOuterStep", 0, 1, 1, double_type, &(config::MaxOuterStep), 1, critical);
 | 
|---|
| 920 |   ParseForParameter(verbose,file,"Deltat", 0, 1, 1, double_type, &(config::Deltat), 1, optional);
 | 
|---|
| 921 |   ParseForParameter(verbose,file,"VisOuterStep", 0, 1, 1, int_type, &(config::OutVisStep), 1, optional);
 | 
|---|
| 922 |   ParseForParameter(verbose,file,"VisSrcOuterStep", 0, 1, 1, int_type, &(config::OutSrcStep), 1, optional);
 | 
|---|
| 923 |   ParseForParameter(verbose,file,"TargetTemp", 0, 1, 1, double_type, &(config::TargetTemp), 1, optional);
 | 
|---|
| 924 |   ParseForParameter(verbose,file,"ScaleTempStep", 0, 1, 1, int_type, &(config::ScaleTempStep), 1, optional);
 | 
|---|
| 925 |   config::EpsWannier = 1e-8;
 | 
|---|
| 926 |   
 | 
|---|
| 927 |   // stop conditions
 | 
|---|
| 928 |   //if (config::MaxOuterStep <= 0) config::MaxOuterStep = 1;
 | 
|---|
| 929 |   ParseForParameter(verbose,file,"MaxPsiStep", 0, 1, 1, int_type, &(config::MaxPsiStep), 1, critical);
 | 
|---|
| 930 |   if (config::MaxPsiStep <= 0) config::MaxPsiStep = 3;
 | 
|---|
| 931 |   
 | 
|---|
| 932 |   ParseForParameter(verbose,file,"MaxMinStep", 0, 1, 1, int_type, &(config::MaxMinStep), 1, critical);
 | 
|---|
| 933 |   ParseForParameter(verbose,file,"MaxMinStep", 0, 2, 1, double_type, &(config::RelEpsTotalEnergy), 1, critical);
 | 
|---|
| 934 |   ParseForParameter(verbose,file,"MaxMinStep", 0, 3, 1, double_type, &(config::RelEpsKineticEnergy), 1, critical);
 | 
|---|
| 935 |   ParseForParameter(verbose,file,"MaxMinStep", 0, 4, 1, int_type, &(config::MaxMinStopStep), 1, critical);
 | 
|---|
| 936 |   if (config::MaxMinStep <= 0) config::MaxMinStep = config::MaxPsiStep;
 | 
|---|
| 937 |   if (config::MaxMinStopStep < 1) config::MaxMinStopStep = 1;
 | 
|---|
| 938 |   config::MaxMinGapStopStep = 1;
 | 
|---|
| 939 |   
 | 
|---|
| 940 |   ParseForParameter(verbose,file,"MaxInitMinStep", 0, 1, 1, int_type, &(config::MaxInitMinStep), 1, critical);
 | 
|---|
| 941 |   ParseForParameter(verbose,file,"MaxInitMinStep", 0, 2, 1, double_type, &(config::InitRelEpsTotalEnergy), 1, critical);
 | 
|---|
| 942 |   ParseForParameter(verbose,file,"MaxInitMinStep", 0, 3, 1, double_type, &(config::InitRelEpsKineticEnergy), 1, critical);
 | 
|---|
| 943 |   ParseForParameter(verbose,file,"MaxInitMinStep", 0, 4, 1, int_type, &(config::InitMaxMinStopStep), 1, critical);
 | 
|---|
| 944 |   if (config::MaxInitMinStep <= 0) config::MaxInitMinStep = config::MaxPsiStep;
 | 
|---|
| 945 |   if (config::InitMaxMinStopStep < 1) config::InitMaxMinStopStep = 1;
 | 
|---|
| 946 |   config::InitMaxMinGapStopStep = 1;
 | 
|---|
| 947 | 
 | 
|---|
| 948 |   ParseForParameter(verbose,file, "BoxLength", 0, 3, 3, lower_trigrid, BoxLength, 1, critical); /* Lattice->RealBasis */
 | 
|---|
| 949 |   mol->cell_size[0] = BoxLength[0];
 | 
|---|
| 950 |   mol->cell_size[1] = BoxLength[3];
 | 
|---|
| 951 |   mol->cell_size[2] = BoxLength[4];
 | 
|---|
| 952 |   mol->cell_size[3] = BoxLength[6];
 | 
|---|
| 953 |   mol->cell_size[4] = BoxLength[7];
 | 
|---|
| 954 |   mol->cell_size[5] = BoxLength[8];
 | 
|---|
| 955 |   if (1) fprintf(stderr,"\n");
 | 
|---|
| 956 |   config::DoPerturbation = 0;
 | 
|---|
| 957 |   config::DoFullCurrent = 0;
 | 
|---|
| 958 | 
 | 
|---|
| 959 |   ParseForParameter(verbose,file,"ECut", 0, 1, 1, double_type, &(config::ECut), 1, critical);
 | 
|---|
| 960 |   ParseForParameter(verbose,file,"MaxLevel", 0, 1, 1, int_type, &(config::MaxLevel), 1, critical);
 | 
|---|
| 961 |   ParseForParameter(verbose,file,"Level0Factor", 0, 1, 1, int_type, &(config::Lev0Factor), 1, critical);
 | 
|---|
| 962 |   if (config::Lev0Factor < 2) {
 | 
|---|
| 963 |     config::Lev0Factor = 2;
 | 
|---|
| 964 |   }
 | 
|---|
| 965 |   ParseForParameter(verbose,file,"RiemannTensor", 0, 1, 1, int_type, &di, 1, critical);
 | 
|---|
| 966 |   if (di >= 0 && di < 2) {
 | 
|---|
| 967 |     config::RiemannTensor = di;
 | 
|---|
| 968 |   } else {
 | 
|---|
| 969 |     fprintf(stderr, "0 <= RiemanTensor < 2: 0 UseNotRT, 1 UseRT");
 | 
|---|
| 970 |     exit(1); 
 | 
|---|
| 971 |   }
 | 
|---|
| 972 |   switch (config::RiemannTensor) {
 | 
|---|
| 973 |     case 0: //UseNoRT
 | 
|---|
| 974 |       if (config::MaxLevel < 2) {
 | 
|---|
| 975 |         config::MaxLevel = 2;
 | 
|---|
| 976 |       }
 | 
|---|
| 977 |       config::LevRFactor = 2;
 | 
|---|
| 978 |       config::RTActualUse = 0;
 | 
|---|
| 979 |       break;
 | 
|---|
| 980 |     case 1: // UseRT
 | 
|---|
| 981 |       if (config::MaxLevel < 3) {
 | 
|---|
| 982 |         config::MaxLevel = 3;
 | 
|---|
| 983 |       }
 | 
|---|
| 984 |       ParseForParameter(verbose,file,"RiemannLevel", 0, 1, 1, int_type, &(config::RiemannLevel), 1, critical);
 | 
|---|
| 985 |       if (config::RiemannLevel < 2) {
 | 
|---|
| 986 |         config::RiemannLevel = 2;
 | 
|---|
| 987 |       } 
 | 
|---|
| 988 |       if (config::RiemannLevel > config::MaxLevel-1) {
 | 
|---|
| 989 |         config::RiemannLevel = config::MaxLevel-1;
 | 
|---|
| 990 |       }
 | 
|---|
| 991 |       ParseForParameter(verbose,file,"LevRFactor", 0, 1, 1, int_type, &(config::LevRFactor), 1, critical);
 | 
|---|
| 992 |       if (config::LevRFactor < 2) {
 | 
|---|
| 993 |         config::LevRFactor = 2;
 | 
|---|
| 994 |       } 
 | 
|---|
| 995 |       config::Lev0Factor = 2;
 | 
|---|
| 996 |       config::RTActualUse = 2;
 | 
|---|
| 997 |       break;
 | 
|---|
| 998 |   }
 | 
|---|
| 999 |   ParseForParameter(verbose,file,"PsiType", 0, 1, 1, int_type, &di, 1, critical);
 | 
|---|
| 1000 |   if (di >= 0 && di < 2) {
 | 
|---|
| 1001 |     config::PsiType = di;
 | 
|---|
| 1002 |   } else {
 | 
|---|
| 1003 |     fprintf(stderr, "0 <= PsiType < 2: 0 UseSpinDouble, 1 UseSpinUpDown");
 | 
|---|
| 1004 |     exit(1); 
 | 
|---|
| 1005 |   }
 | 
|---|
| 1006 |   switch (config::PsiType) {
 | 
|---|
| 1007 |   case 0: // SpinDouble
 | 
|---|
| 1008 |     ParseForParameter(verbose,file,"MaxPsiDouble", 0, 1, 1, int_type, &(config::MaxPsiDouble), 1, critical);
 | 
|---|
| 1009 |     config::AddPsis = 0;
 | 
|---|
| 1010 |     break;
 | 
|---|
| 1011 |   case 1: // SpinUpDown
 | 
|---|
| 1012 |     if (config::ProcPEGamma % 2) config::ProcPEGamma*=2;
 | 
|---|
| 1013 |     ParseForParameter(verbose,file,"MaxPsiUp", 0, 1, 1, int_type, &(config::PsiMaxNoUp), 1, critical);
 | 
|---|
| 1014 |     ParseForParameter(verbose,file,"MaxPsiDown", 0, 1, 1, int_type, &(config::PsiMaxNoDown), 1, critical);
 | 
|---|
| 1015 |     config::AddPsis = 0;
 | 
|---|
| 1016 |     break;
 | 
|---|
| 1017 |   }
 | 
|---|
| 1018 |   
 | 
|---|
| 1019 |   // IonsInitRead
 | 
|---|
| 1020 |   
 | 
|---|
| 1021 |   ParseForParameter(verbose,file,"RCut", 0, 1, 1, double_type, &(config::RCut), 1, critical);
 | 
|---|
| 1022 |   ParseForParameter(verbose,file,"IsAngstroem", 0, 1, 1, int_type, &(config::IsAngstroem), 1, critical);
 | 
|---|
| 1023 |   config::RelativeCoord = 0;
 | 
|---|
| 1024 |   config::StructOpt = 0;
 | 
|---|
| 1025 | 
 | 
|---|
| 1026 |   // Routine from builder.cpp
 | 
|---|
| 1027 |   
 | 
|---|
| 1028 |   
 | 
|---|
| 1029 |   for (i=MAX_ELEMENTS;i--;) 
 | 
|---|
| 1030 |     elementhash[i] = NULL;
 | 
|---|
| 1031 |   cout << Verbose(0) << "Parsing Ions ..." << endl;
 | 
|---|
| 1032 |   No=0;
 | 
|---|
| 1033 |   found = 0;
 | 
|---|
| 1034 |   while (getline(*file,zeile,'\n')) {
 | 
|---|
| 1035 |     if (zeile.find("Ions_Data") == 0) {
 | 
|---|
| 1036 |       cout << Verbose(1) << "found Ions_Data...begin parsing" << endl;
 | 
|---|
| 1037 |       found ++;
 | 
|---|
| 1038 |     }
 | 
|---|
| 1039 |     if (found > 0) {
 | 
|---|
| 1040 |       if (zeile.find("Ions_Data") == 0) 
 | 
|---|
| 1041 |         getline(*file,zeile,'\n'); // read next line and parse this one
 | 
|---|
| 1042 |       istringstream input(zeile);
 | 
|---|
| 1043 |       input >> AtomNo;  // number of atoms
 | 
|---|
| 1044 |       input >> Z;       // atomic number
 | 
|---|
| 1045 |       input >> a;
 | 
|---|
| 1046 |       input >> l;
 | 
|---|
| 1047 |       input >> l;
 | 
|---|
| 1048 |       input >> b;     // element mass
 | 
|---|
| 1049 |       elementhash[No] = periode->FindElement(Z);
 | 
|---|
| 1050 |       cout << Verbose(1) << "AtomNo: " << AtomNo << "\tZ: " << Z << "\ta:" << a << "\tl:"  << l << "\b:" << b << "\tElement:" << elementhash[No] << "\t:" << endl;
 | 
|---|
| 1051 |       for(i=0;i<AtomNo;i++) {
 | 
|---|
| 1052 |         if (!getline(*file,zeile,'\n')) {// parse on and on
 | 
|---|
| 1053 |           cout << Verbose(2) << "Error: Too few items in ionic list of element" << elementhash[No] << "." << endl << "Exiting." << endl;
 | 
|---|
| 1054 |           // return 1;
 | 
|---|
| 1055 |         } else {
 | 
|---|
| 1056 |           //cout << Verbose(2) << "Reading line: " << zeile << endl;
 | 
|---|
| 1057 |         }
 | 
|---|
| 1058 |         istringstream input2(zeile);
 | 
|---|
| 1059 |         atom *neues = new atom();
 | 
|---|
| 1060 |         input2 >> neues->x.x[0]; // x
 | 
|---|
| 1061 |         input2 >> neues->x.x[1]; // y
 | 
|---|
| 1062 |         input2 >> neues->x.x[2]; // z
 | 
|---|
| 1063 |         input2 >> l;
 | 
|---|
| 1064 |         neues->type = elementhash[No]; // find element type
 | 
|---|
| 1065 |         mol->AddAtom(neues);
 | 
|---|
| 1066 |       }
 | 
|---|
| 1067 |       No++;
 | 
|---|
| 1068 |     }
 | 
|---|
| 1069 |   }   
 | 
|---|
| 1070 |   file->close();
 | 
|---|
| 1071 |   delete(file);
 | 
|---|
| 1072 | };
 | 
|---|
| 1073 | 
 | 
|---|
| 1074 | /** Stores all elements of config structure from which they can be re-read.
 | 
|---|
| 1075 |  * \param output open output *file stream to write to
 | 
|---|
| 1076 |  * \param *periode pointer to a periodentafel class with all elements
 | 
|---|
| 1077 |  * \param *mol pointer to molecule containing all atoms of the molecule 
 | 
|---|
| 1078 |  */
 | 
|---|
| 1079 | bool config::Save(ofstream *output, periodentafel *periode, molecule *mol) const
 | 
|---|
| 1080 | {
 | 
|---|
| 1081 |   bool result = true;
 | 
|---|
| 1082 |         // bring MaxTypes up to date
 | 
|---|
| 1083 |         mol->CountElements();
 | 
|---|
| 1084 |   if (output != NULL) {
 | 
|---|
| 1085 |     *output << "# ParallelCarParinello - main configuration file - created with molecuilder" << endl;
 | 
|---|
| 1086 |     *output << endl;
 | 
|---|
| 1087 |     *output << "mainname\t" << config::mainname << "\t# programm name (for runtime files)" << endl;
 | 
|---|
| 1088 |     *output << "defaultpath\t" << config::defaultpath << "\t# where to put files during runtime" << endl;
 | 
|---|
| 1089 |     *output << "pseudopotpath\t" << config::pseudopotpath << "\t# where to find pseudopotentials" << endl;
 | 
|---|
| 1090 |     *output << endl;
 | 
|---|
| 1091 |     *output << "ProcPEGamma\t" << config::ProcPEGamma << "\t# for parallel computing: share constants" << endl;
 | 
|---|
| 1092 |     *output << "ProcPEPsi\t" << config::ProcPEPsi << "\t# for parallel computing: share wave functions" << endl;
 | 
|---|
| 1093 |     *output << "DoOutVis\t" << config::DoOutVis << "\t# Output data for OpenDX" << endl;
 | 
|---|
| 1094 |     *output << "DoOutMes\t" << config::DoOutMes << "\t# Output data for measurements" << endl;
 | 
|---|
| 1095 |     *output << "DoOutOrbitals\t" << config::DoOutOrbitals << "\t# Output all Orbitals" << endl;
 | 
|---|
| 1096 |     *output << "DoOutCurr\t" << config::DoOutCurrent << "\t# Ouput current density for OpenDx" << endl;
 | 
|---|
| 1097 |     *output << "DoOutNICS\t" << config::DoOutNICS << "\t# Output Nucleus independent current shieldings" << endl;
 | 
|---|
| 1098 |     *output << "DoPerturbation\t" << config::DoPerturbation << "\t# Do perturbation calculate and determine susceptibility and shielding" << endl;
 | 
|---|
| 1099 |     *output << "DoFullCurrent\t" << config::DoFullCurrent << "\t# Do full perturbation" << endl;
 | 
|---|
| 1100 |     *output << "DoConstrainedMD\t" << config::DoConstrainedMD << "\t# Do perform a constrained (>0, relating to current MD step) instead of unconstrained (0) MD" << endl;
 | 
|---|
| 1101 |     *output << "Thermostat\t" << ThermostatNames[Thermostat] << "\t";
 | 
|---|
| 1102 |     switch(Thermostat) {
 | 
|---|
| 1103 |       default:
 | 
|---|
| 1104 |       case None:
 | 
|---|
| 1105 |         break;
 | 
|---|
| 1106 |       case Woodcock:
 | 
|---|
| 1107 |         *output << ScaleTempStep;
 | 
|---|
| 1108 |         break;
 | 
|---|
| 1109 |       case Gaussian:
 | 
|---|
| 1110 |         *output << ScaleTempStep;
 | 
|---|
| 1111 |         break;
 | 
|---|
| 1112 |       case Langevin:
 | 
|---|
| 1113 |         *output << TempFrequency << "\t" << alpha;
 | 
|---|
| 1114 |         break;
 | 
|---|
| 1115 |       case Berendsen:
 | 
|---|
| 1116 |         *output << TempFrequency;
 | 
|---|
| 1117 |         break;
 | 
|---|
| 1118 |       case NoseHoover:
 | 
|---|
| 1119 |         *output << HooverMass;
 | 
|---|
| 1120 |         break;
 | 
|---|
| 1121 |     };
 | 
|---|
| 1122 |     *output << "\t# Which Thermostat and its parameters to use in MD case." << endl;
 | 
|---|
| 1123 |     *output << "CommonWannier\t" << config::CommonWannier << "\t# Put virtual centers at indivual orbits, all common, merged by variance, to grid point, to cell center" << endl;
 | 
|---|
| 1124 |     *output << "SawtoothStart\t" << config::SawtoothStart << "\t# Absolute value for smooth transition at cell border " << endl;
 | 
|---|
| 1125 |     *output << "VectorPlane\t" << config::VectorPlane << "\t# Cut plane axis (x, y or z: 0,1,2) for two-dim current vector plot" << endl;
 | 
|---|
| 1126 |     *output << "VectorCut\t" << config::VectorCut << "\t# Cut plane axis value" << endl;
 | 
|---|
| 1127 |     *output << "AddGramSch\t" << config::UseAddGramSch << "\t# Additional GramSchmidtOrtogonalization to be safe" << endl;
 | 
|---|
| 1128 |     *output << "Seed\t\t" << config::Seed << "\t# initial value for random seed for Psi coefficients" << endl;
 | 
|---|
| 1129 |     *output << endl;
 | 
|---|
| 1130 |     *output << "MaxOuterStep\t" << config::MaxOuterStep << "\t# number of MolecularDynamics/Structure optimization steps" << endl;
 | 
|---|
| 1131 |     *output << "Deltat\t" << config::Deltat << "\t# time per MD step" << endl;
 | 
|---|
| 1132 |     *output << "OutVisStep\t" << config::OutVisStep << "\t# Output visual data every ...th step" << endl;
 | 
|---|
| 1133 |     *output << "OutSrcStep\t" << config::OutSrcStep << "\t# Output \"restart\" data every ..th step" << endl;
 | 
|---|
| 1134 |     *output << "TargetTemp\t" << config::TargetTemp << "\t# Target temperature" << endl;
 | 
|---|
| 1135 |     *output << "MaxPsiStep\t" << config::MaxPsiStep << "\t# number of Minimisation steps per state (0 - default)" << endl;
 | 
|---|
| 1136 |     *output << "EpsWannier\t" << config::EpsWannier << "\t# tolerance value for spread minimisation of orbitals" << endl;
 | 
|---|
| 1137 |     *output << endl;
 | 
|---|
| 1138 |     *output << "# Values specifying when to stop" << endl;
 | 
|---|
| 1139 |     *output << "MaxMinStep\t" << config::MaxMinStep << "\t# Maximum number of steps" << endl;
 | 
|---|
| 1140 |     *output << "RelEpsTotalE\t" << config::RelEpsTotalEnergy << "\t# relative change in total energy" << endl;
 | 
|---|
| 1141 |     *output << "RelEpsKineticE\t" << config::RelEpsKineticEnergy << "\t# relative change in kinetic energy" << endl;
 | 
|---|
| 1142 |     *output << "MaxMinStopStep\t" << config::MaxMinStopStep << "\t# check every ..th steps" << endl;
 | 
|---|
| 1143 |     *output << "MaxMinGapStopStep\t" << config::MaxMinGapStopStep << "\t# check every ..th steps" << endl;
 | 
|---|
| 1144 |     *output << endl;
 | 
|---|
| 1145 |     *output << "# Values specifying when to stop for INIT, otherwise same as above" << endl;
 | 
|---|
| 1146 |     *output << "MaxInitMinStep\t" << config::MaxInitMinStep << "\t# Maximum number of steps" << endl;
 | 
|---|
| 1147 |     *output << "InitRelEpsTotalE\t" << config::InitRelEpsTotalEnergy << "\t# relative change in total energy" << endl;
 | 
|---|
| 1148 |     *output << "InitRelEpsKineticE\t" << config::InitRelEpsKineticEnergy << "\t# relative change in kinetic energy" << endl;
 | 
|---|
| 1149 |     *output << "InitMaxMinStopStep\t" << config::InitMaxMinStopStep << "\t# check every ..th steps" << endl;
 | 
|---|
| 1150 |     *output << "InitMaxMinGapStopStep\t" << config::InitMaxMinGapStopStep << "\t# check every ..th steps" << endl;
 | 
|---|
| 1151 |     *output << endl;
 | 
|---|
| 1152 |     *output << "BoxLength\t\t\t# (Length of a unit cell)" << endl;
 | 
|---|
| 1153 |     *output << mol->cell_size[0] << "\t" << endl;
 | 
|---|
| 1154 |     *output << mol->cell_size[1] << "\t" << mol->cell_size[2] << "\t" << endl;
 | 
|---|
| 1155 |     *output << mol->cell_size[3] << "\t" << mol->cell_size[4] << "\t" << mol->cell_size[5] << "\t" << endl;
 | 
|---|
| 1156 |     // FIXME
 | 
|---|
| 1157 |     *output << endl;
 | 
|---|
| 1158 |     *output << "ECut\t\t" << config::ECut << "\t# energy cutoff for discretization in Hartrees" << endl;
 | 
|---|
| 1159 |     *output << "MaxLevel\t" << config::MaxLevel << "\t# number of different levels in the code, >=2" << endl;
 | 
|---|
| 1160 |     *output << "Level0Factor\t" << config::Lev0Factor << "\t# factor by which node number increases from S to 0 level" << endl;
 | 
|---|
| 1161 |     *output << "RiemannTensor\t" << config::RiemannTensor << "\t# (Use metric)" << endl;
 | 
|---|
| 1162 |     switch (config::RiemannTensor) {
 | 
|---|
| 1163 |       case 0: //UseNoRT
 | 
|---|
| 1164 |         break;
 | 
|---|
| 1165 |       case 1: // UseRT
 | 
|---|
| 1166 |         *output << "RiemannLevel\t" << config::RiemannLevel << "\t# Number of Riemann Levels" << endl;
 | 
|---|
| 1167 |         *output << "LevRFactor\t" << config::LevRFactor << "\t# factor by which node number increases from 0 to R level from" << endl;
 | 
|---|
| 1168 |         break;
 | 
|---|
| 1169 |     }
 | 
|---|
| 1170 |     *output << "PsiType\t\t" << config::PsiType << "\t# 0 - doubly occupied, 1 - SpinUp,SpinDown" << endl;
 | 
|---|
| 1171 |     // write out both types for easier changing afterwards
 | 
|---|
| 1172 |   //  switch (PsiType) {
 | 
|---|
| 1173 |   //    case 0:
 | 
|---|
| 1174 |         *output << "MaxPsiDouble\t" << config::MaxPsiDouble << "\t# here: specifying both maximum number of SpinUp- and -Down-states" << endl;
 | 
|---|
| 1175 |   //      break;
 | 
|---|
| 1176 |   //    case 1:
 | 
|---|
| 1177 |         *output << "PsiMaxNoUp\t" << config::PsiMaxNoUp << "\t# here: specifying maximum number of SpinUp-states" << endl;
 | 
|---|
| 1178 |         *output << "PsiMaxNoDown\t" << config::PsiMaxNoDown << "\t# here: specifying maximum number of SpinDown-states" << endl;
 | 
|---|
| 1179 |   //      break;
 | 
|---|
| 1180 |   //  }
 | 
|---|
| 1181 |     *output << "AddPsis\t\t" << config::AddPsis << "\t# Additional unoccupied Psis for bandgap determination" << endl;
 | 
|---|
| 1182 |     *output << endl;
 | 
|---|
| 1183 |     *output << "RCut\t\t" << config::RCut << "\t# R-cut for the ewald summation" << endl;
 | 
|---|
| 1184 |     *output << "StructOpt\t" << config::StructOpt << "\t# Do structure optimization beforehand" << endl;
 | 
|---|
| 1185 |     *output << "IsAngstroem\t" << config::IsAngstroem << "\t# 0 - Bohr, 1 - Angstroem" << endl;
 | 
|---|
| 1186 |     *output << "RelativeCoord\t" << config::RelativeCoord << "\t# whether ion coordinates are relative (1) or absolute (0)" << endl;
 | 
|---|
| 1187 |     *output << "MaxTypes\t" << mol->ElementCount <<  "\t# maximum number of different ion types" << endl;
 | 
|---|
| 1188 |     *output << endl;
 | 
|---|
| 1189 |     result = result && mol->Checkout(output);
 | 
|---|
| 1190 |     if (mol->MDSteps <=1 )
 | 
|---|
| 1191 |       result = result && mol->Output(output);
 | 
|---|
| 1192 |     else
 | 
|---|
| 1193 |       result = result && mol->OutputTrajectories(output);
 | 
|---|
| 1194 |     return result;
 | 
|---|
| 1195 |   } else
 | 
|---|
| 1196 |     return false;
 | 
|---|
| 1197 | };
 | 
|---|
| 1198 | 
 | 
|---|
| 1199 | /** Stores all elements in a MPQC input file.
 | 
|---|
| 1200 |  * Note that this format cannot be parsed again.
 | 
|---|
| 1201 |  * \param output open output *file stream to write to
 | 
|---|
| 1202 |  * \param *mol pointer to molecule containing all atoms of the molecule 
 | 
|---|
| 1203 |  */
 | 
|---|
| 1204 | bool config::SaveMPQC(ofstream *output, molecule *mol) const
 | 
|---|
| 1205 | {
 | 
|---|
| 1206 |   int ElementNo = 0;
 | 
|---|
| 1207 |   int AtomNo;
 | 
|---|
| 1208 |   atom *Walker = NULL;
 | 
|---|
| 1209 |   element *runner = mol->elemente->start;
 | 
|---|
| 1210 |   Vector *center = NULL;
 | 
|---|
| 1211 | 
 | 
|---|
| 1212 |   *output << "% Created by MoleCuilder" << endl;
 | 
|---|
| 1213 |   *output << "mpqc: (" << endl;
 | 
|---|
| 1214 |   *output << "\tsavestate = no" << endl;
 | 
|---|
| 1215 |   *output << "\tdo_gradient = yes" << endl;
 | 
|---|
| 1216 |   *output << "\tmole<CLHF>: (" << endl;
 | 
|---|
| 1217 |   *output << "\t\tmolecule<Molecule>: (" << endl;
 | 
|---|
| 1218 |   *output << "\t\t\tunit = " << (IsAngstroem ? "angstrom" : "bohr" ) << endl;
 | 
|---|
| 1219 |   *output << "\t\t\t{ atoms geometry } = {" << endl;
 | 
|---|
| 1220 |   center = mol->DetermineCenterOfAll(output);
 | 
|---|
| 1221 |   // output of atoms
 | 
|---|
| 1222 |   while (runner->next != mol->elemente->end) { // go through every element
 | 
|---|
| 1223 |     runner = runner->next;
 | 
|---|
| 1224 |     if (mol->ElementsInMolecule[runner->Z]) { // if this element got atoms
 | 
|---|
| 1225 |       ElementNo++;
 | 
|---|
| 1226 |       AtomNo = 0;
 | 
|---|
| 1227 |       Walker = mol->start;
 | 
|---|
| 1228 |       while (Walker->next != mol->end) { // go through every atom of this element
 | 
|---|
| 1229 |         Walker = Walker->next;
 | 
|---|
| 1230 |         if (Walker->type == runner) { // if this atom fits to element
 | 
|---|
| 1231 |           AtomNo++;
 | 
|---|
| 1232 |           *output << "\t\t\t\t" << Walker->type->symbol << " [ " << Walker->x.x[0]-center->x[0] << "\t" << Walker->x.x[1]-center->x[1] << "\t" << Walker->x.x[2]-center->x[2] << " ]" << endl;
 | 
|---|
| 1233 |         }
 | 
|---|
| 1234 |       }
 | 
|---|
| 1235 |     }
 | 
|---|
| 1236 |   }
 | 
|---|
| 1237 |   delete(center);
 | 
|---|
| 1238 |   *output << "\t\t\t}" << endl;
 | 
|---|
| 1239 |   *output << "\t\t)" << endl;
 | 
|---|
| 1240 |   *output << "\t\tbasis<GaussianBasisSet>: (" << endl;
 | 
|---|
| 1241 |   *output << "\t\t\tname = \"STO-3G\"" << endl;
 | 
|---|
| 1242 |   *output << "\t\t\tmolecule = $:mpqc:mole:molecule" << endl;
 | 
|---|
| 1243 |   *output << "\t\t)" << endl;
 | 
|---|
| 1244 |   *output << "\t)" << endl;
 | 
|---|
| 1245 |   *output << ")" << endl;
 | 
|---|
| 1246 |   return true;
 | 
|---|
| 1247 | };
 | 
|---|
| 1248 | 
 | 
|---|
| 1249 | /** Reads parameter from a parsed file.
 | 
|---|
| 1250 |  * The file is either parsed for a certain keyword or if null is given for
 | 
|---|
| 1251 |  * the value in row yth and column xth. If the keyword was necessity#critical,
 | 
|---|
| 1252 |  * then an error is thrown and the programme aborted.
 | 
|---|
| 1253 |  * \warning value is modified (both in contents and position)!
 | 
|---|
| 1254 |  * \param verbose 1 - print found value to stderr, 0 - don't
 | 
|---|
| 1255 |  * \param file file to be parsed
 | 
|---|
| 1256 |  * \param name Name of value in file (at least 3 chars!)
 | 
|---|
| 1257 |  * \param sequential 1 - do not reset file pointer to begin of file, 0 - set to beginning 
 | 
|---|
| 1258 |  *        (if file is sequentially parsed this can be way faster! However, beware of multiple values per line, as whole line is read -
 | 
|---|
| 1259 |  *         best approach: 0 0 0 1 (not resetted only on last value of line) - and of yth, which is now
 | 
|---|
| 1260 |  *         counted from this unresetted position!)
 | 
|---|
| 1261 |  * \param xth Which among a number of parameters it is (in grid case it's row number as grid is read as a whole!)
 | 
|---|
| 1262 |  * \param yth In grid case specifying column number, otherwise the yth \a name matching line
 | 
|---|
| 1263 |  * \param type Type of the Parameter to be read
 | 
|---|
| 1264 |  * \param value address of the value to be read (must have been allocated)
 | 
|---|
| 1265 |  * \param repetition determines, if the keyword appears multiply in the config file, which repetition shall be parsed, i.e. 1 if not multiply
 | 
|---|
| 1266 |  * \param critical necessity of this keyword being specified (optional, critical)
 | 
|---|
| 1267 |  * \return 1 - found, 0 - not found
 | 
|---|
| 1268 |  * \note Routine is taken from the pcp project and hack-a-slack adapted to C++
 | 
|---|
| 1269 |  */
 | 
|---|
| 1270 | int config::ParseForParameter(int verbose, ifstream *file, const char *name, int sequential, int const xth, int const yth, int type, void *value, int repetition, int critical) {
 | 
|---|
| 1271 |   int i,j;  // loop variables
 | 
|---|
| 1272 |   int length = 0, maxlength = -1;
 | 
|---|
| 1273 |   long file_position = file->tellg(); // mark current position
 | 
|---|
| 1274 |   char *dummy1, *dummy, *free_dummy;    // pointers in the line that is read in per step
 | 
|---|
| 1275 |   dummy1 = free_dummy = (char *) Malloc(256 * sizeof(char), "config::ParseForParameter: *free_dummy");
 | 
|---|
| 1276 | 
 | 
|---|
| 1277 |   //fprintf(stderr,"Parsing for %s\n",name);  
 | 
|---|
| 1278 |   if (repetition == 0)
 | 
|---|
| 1279 |     //Error(SomeError, "ParseForParameter(): argument repetition must not be 0!");
 | 
|---|
| 1280 |     return 0;
 | 
|---|
| 1281 | 
 | 
|---|
| 1282 |   int line = 0; // marks line where parameter was found
 | 
|---|
| 1283 |   int found = (type >= grid) ? 0 : (-yth + 1);  // marks if yth parameter name was found
 | 
|---|
| 1284 |   while((found != repetition)) {
 | 
|---|
| 1285 |     dummy1 = dummy = free_dummy;
 | 
|---|
| 1286 |     do {
 | 
|---|
| 1287 |       file->getline(dummy1, 256); // Read the whole line
 | 
|---|
| 1288 |       if (file->eof()) {
 | 
|---|
| 1289 |         if ((critical) && (found == 0)) {
 | 
|---|
| 1290 |           Free((void **)&free_dummy, "config::ParseForParameter: *free_dummy");
 | 
|---|
| 1291 |           //Error(InitReading, name);
 | 
|---|
| 1292 |           fprintf(stderr,"Error:InitReading, critical %s not found\n", name);
 | 
|---|
| 1293 |           exit(255);
 | 
|---|
| 1294 |         } else {
 | 
|---|
| 1295 |           //if (!sequential)
 | 
|---|
| 1296 |           file->clear();
 | 
|---|
| 1297 |           file->seekg(file_position, ios::beg);  // rewind to start position
 | 
|---|
| 1298 |           Free((void **)&free_dummy, "config::ParseForParameter: *free_dummy");          
 | 
|---|
| 1299 |           return 0;
 | 
|---|
| 1300 |         }
 | 
|---|
| 1301 |       }
 | 
|---|
| 1302 |       line++;
 | 
|---|
| 1303 |     } while (dummy != NULL && dummy1 != NULL && ((dummy1[0] == '#') || (dummy1[0] == '\0'))); // skip commentary and empty lines
 | 
|---|
| 1304 |     
 | 
|---|
| 1305 |     // C++ getline removes newline at end, thus re-add
 | 
|---|
| 1306 |     if ((dummy1 != NULL) && (strchr(dummy1,'\n') == NULL)) {
 | 
|---|
| 1307 |       i = strlen(dummy1);
 | 
|---|
| 1308 |       dummy1[i] = '\n';
 | 
|---|
| 1309 |       dummy1[i+1] = '\0';
 | 
|---|
| 1310 |     }
 | 
|---|
| 1311 |     //fprintf(stderr,"line %i ends at %i, newline at %i\n", line, strlen(dummy1), strchr(dummy1,'\n')-free_dummy);
 | 
|---|
| 1312 | 
 | 
|---|
| 1313 |     if (dummy1 == NULL) {
 | 
|---|
| 1314 |       if (verbose) fprintf(stderr,"Error reading line %i\n",line);
 | 
|---|
| 1315 |     } else {
 | 
|---|
| 1316 |       //fprintf(stderr,"Now parsing the line %i: %s\n", line, dummy1);
 | 
|---|
| 1317 |     }
 | 
|---|
| 1318 |     // Seek for possible end of keyword on line if given ...
 | 
|---|
| 1319 |     if (name != NULL) {
 | 
|---|
| 1320 |       dummy = strchr(dummy1,'\t');  // set dummy on first tab or space which ever's nearer
 | 
|---|
| 1321 |       if (dummy == NULL) {
 | 
|---|
| 1322 |         dummy = strchr(dummy1, ' ');  // if not found seek for space
 | 
|---|
| 1323 |         while ((dummy != NULL) && ((*dummy == '\t') || (*dummy == ' ')))    // skip some more tabs and spaces if necessary
 | 
|---|
| 1324 |           dummy++;
 | 
|---|
| 1325 |       }
 | 
|---|
| 1326 |       if (dummy == NULL) {
 | 
|---|
| 1327 |         dummy = strchr(dummy1, '\n'); // set on line end then (whole line = keyword)
 | 
|---|
| 1328 |         //fprintf(stderr,"Error: Cannot find tabs or spaces on line %i in search for %s\n", line, name);
 | 
|---|
| 1329 |         //Free((void **)&free_dummy);
 | 
|---|
| 1330 |         //Error(FileOpenParams, NULL);      
 | 
|---|
| 1331 |       } else {
 | 
|---|
| 1332 |         //fprintf(stderr,"found tab at %i\n",(char *)dummy-(char *)dummy1);
 | 
|---|
| 1333 |       }
 | 
|---|
| 1334 |     } else dummy = dummy1;
 | 
|---|
| 1335 |     // ... and check if it is the keyword!
 | 
|---|
| 1336 |     //fprintf(stderr,"name %p, dummy %i/%c, dummy1 %i/%c, strlen(name) %i\n", &name, dummy, *dummy, dummy1, *dummy1, strlen(name));
 | 
|---|
| 1337 |     if ((name == NULL) || (((dummy-dummy1 >= 3) && (strncmp(dummy1, name, strlen(name)) == 0)) && ((unsigned int)(dummy-dummy1) == strlen(name)))) {
 | 
|---|
| 1338 |       found++; // found the parameter!
 | 
|---|
| 1339 |       //fprintf(stderr,"found %s at line %i between %i and %i\n", name, line, dummy1, dummy);    
 | 
|---|
| 1340 |       
 | 
|---|
| 1341 |       if (found == repetition) {
 | 
|---|
| 1342 |         for (i=0;i<xth;i++) { // i = rows
 | 
|---|
| 1343 |           if (type >= grid) {
 | 
|---|
| 1344 |             // grid structure means that grid starts on the next line, not right after keyword
 | 
|---|
| 1345 |             dummy1 = dummy = free_dummy;
 | 
|---|
| 1346 |             do {
 | 
|---|
| 1347 |               file->getline(dummy1, 256); // Read the whole line, skip commentary and empty ones
 | 
|---|
| 1348 |               if (file->eof()) {
 | 
|---|
| 1349 |                 if ((critical) && (found == 0)) {
 | 
|---|
| 1350 |                   Free((void **)&free_dummy, "config::ParseForParameter: *free_dummy");
 | 
|---|
| 1351 |                   //Error(InitReading, name);
 | 
|---|
| 1352 |                   fprintf(stderr,"Error:InitReading, critical %s not found\n", name);
 | 
|---|
| 1353 |                   exit(255);
 | 
|---|
| 1354 |                 } else {
 | 
|---|
| 1355 |                   //if (!sequential)
 | 
|---|
| 1356 |                   file->clear();
 | 
|---|
| 1357 |                   file->seekg(file_position, ios::beg);  // rewind to start position
 | 
|---|
| 1358 |                   Free((void **)&free_dummy, "config::ParseForParameter: *free_dummy");
 | 
|---|
| 1359 |                   return 0;
 | 
|---|
| 1360 |                 }
 | 
|---|
| 1361 |               }
 | 
|---|
| 1362 |               line++;
 | 
|---|
| 1363 |             } while ((dummy1[0] == '#') || (dummy1[0] == '\n'));
 | 
|---|
| 1364 |             if (dummy1 == NULL){
 | 
|---|
| 1365 |               if (verbose) fprintf(stderr,"Error reading line %i\n", line);
 | 
|---|
| 1366 |             } else {
 | 
|---|
| 1367 |               //fprintf(stderr,"Reading next line %i: %s\n", line, dummy1);
 | 
|---|
| 1368 |             }
 | 
|---|
| 1369 |           } else { // simple int, strings or doubles start in the same line
 | 
|---|
| 1370 |             while ((*dummy == '\t') || (*dummy == ' '))   // skip interjacent tabs and spaces
 | 
|---|
| 1371 |               dummy++;
 | 
|---|
| 1372 |           }
 | 
|---|
| 1373 |           // C++ getline removes newline at end, thus re-add
 | 
|---|
| 1374 |           if ((dummy1 != NULL) && (strchr(dummy1,'\n') == NULL)) {
 | 
|---|
| 1375 |             j = strlen(dummy1);
 | 
|---|
| 1376 |             dummy1[j] = '\n';
 | 
|---|
| 1377 |             dummy1[j+1] = '\0';
 | 
|---|
| 1378 |           }
 | 
|---|
| 1379 |   
 | 
|---|
| 1380 |           int start = (type >= grid) ? 0 : yth-1 ;
 | 
|---|
| 1381 |           for (j=start;j<yth;j++) { // j = columns
 | 
|---|
| 1382 |             // check for lower triangular area and upper triangular area
 | 
|---|
| 1383 |             if ( ((i > j) && (type == upper_trigrid)) || ((j > i) && (type == lower_trigrid))) {
 | 
|---|
| 1384 |               *((double *)value) = 0.0;
 | 
|---|
| 1385 |               fprintf(stderr,"%f\t",*((double *)value));
 | 
|---|
| 1386 |               value = (void *)((long)value + sizeof(double));
 | 
|---|
| 1387 |               //value += sizeof(double);
 | 
|---|
| 1388 |             } else {
 | 
|---|
| 1389 |               // otherwise we must skip all interjacent tabs and spaces and find next value
 | 
|---|
| 1390 |               dummy1 = dummy;
 | 
|---|
| 1391 |               dummy = strchr(dummy1, '\t'); // seek for tab or space
 | 
|---|
| 1392 |               if (dummy == NULL)
 | 
|---|
| 1393 |                 dummy = strchr(dummy1, ' ');  // if not found seek for space
 | 
|---|
| 1394 |               if (dummy == NULL) { // if still zero returned ...
 | 
|---|
| 1395 |                 dummy = strchr(dummy1, '\n');  // ... at line end then
 | 
|---|
| 1396 |                 if ((j < yth-1) && (type < 4)) {  // check if xth value or not yet
 | 
|---|
| 1397 |                   if (critical) {
 | 
|---|
| 1398 |                     if (verbose) fprintf(stderr,"Error: EoL at %i and still missing %i value(s) for parameter %s\n", line, yth-j, name);
 | 
|---|
| 1399 |                     Free((void **)&free_dummy, "config::ParseForParameter: *free_dummy");
 | 
|---|
| 1400 |                     //return 0;
 | 
|---|
| 1401 |                     exit(255);
 | 
|---|
| 1402 |                     //Error(FileOpenParams, NULL);      
 | 
|---|
| 1403 |                   } else {
 | 
|---|
| 1404 |                     //if (!sequential)
 | 
|---|
| 1405 |                     file->clear();
 | 
|---|
| 1406 |                     file->seekg(file_position, ios::beg);  // rewind to start position
 | 
|---|
| 1407 |                     Free((void **)&free_dummy, "config::ParseForParameter: *free_dummy");
 | 
|---|
| 1408 |                     return 0;
 | 
|---|
| 1409 |                   }
 | 
|---|
| 1410 |                 }
 | 
|---|
| 1411 |               } else {
 | 
|---|
| 1412 |                 //fprintf(stderr,"found tab at %i\n",(char *)dummy-(char *)free_dummy);
 | 
|---|
| 1413 |               }
 | 
|---|
| 1414 |               if (*dummy1 == '#') {
 | 
|---|
| 1415 |                 // found comment, skipping rest of line
 | 
|---|
| 1416 |                 //if (verbose) fprintf(stderr,"Error: '#' at %i and still missing %i value(s) for parameter %s\n", line, yth-j, name);
 | 
|---|
| 1417 |                 if (!sequential) { // here we need it! 
 | 
|---|
| 1418 |                   file->seekg(file_position, ios::beg);  // rewind to start position
 | 
|---|
| 1419 |                 }
 | 
|---|
| 1420 |                 Free((void **)&free_dummy, "config::ParseForParameter: *free_dummy");
 | 
|---|
| 1421 |                 return 0;
 | 
|---|
| 1422 |               }
 | 
|---|
| 1423 |               //fprintf(stderr,"value from %i to %i\n",(char *)dummy1-(char *)free_dummy,(char *)dummy-(char *)free_dummy);
 | 
|---|
| 1424 |               switch(type) {
 | 
|---|
| 1425 |                 case (row_int):
 | 
|---|
| 1426 |                   *((int *)value) = atoi(dummy1);
 | 
|---|
| 1427 |                   if ((verbose) && (i==0) && (j==0)) fprintf(stderr,"%s = ", name);
 | 
|---|
| 1428 |                   if (verbose) fprintf(stderr,"%i\t",*((int *)value));
 | 
|---|
| 1429 |                     value = (void *)((long)value + sizeof(int));
 | 
|---|
| 1430 |                     //value += sizeof(int);
 | 
|---|
| 1431 |                   break;
 | 
|---|
| 1432 |                 case(row_double): 
 | 
|---|
| 1433 |                 case(grid):
 | 
|---|
| 1434 |                 case(lower_trigrid):
 | 
|---|
| 1435 |                 case(upper_trigrid):
 | 
|---|
| 1436 |                   *((double *)value) = atof(dummy1);
 | 
|---|
| 1437 |                   if ((verbose) && (i==0) && (j==0)) fprintf(stderr,"%s = ", name);
 | 
|---|
| 1438 |                   if (verbose) fprintf(stderr,"%lg\t",*((double *)value));
 | 
|---|
| 1439 |                   value = (void *)((long)value + sizeof(double));
 | 
|---|
| 1440 |                   //value += sizeof(double);
 | 
|---|
| 1441 |                   break;
 | 
|---|
| 1442 |                 case(double_type):
 | 
|---|
| 1443 |                   *((double *)value) = atof(dummy1);
 | 
|---|
| 1444 |                   if ((verbose) && (i == xth-1)) fprintf(stderr,"%s = %lg\n", name, *((double *) value));
 | 
|---|
| 1445 |                   //value += sizeof(double);
 | 
|---|
| 1446 |                   break;
 | 
|---|
| 1447 |                 case(int_type):
 | 
|---|
| 1448 |                   *((int *)value) = atoi(dummy1);
 | 
|---|
| 1449 |                   if ((verbose) && (i == xth-1)) fprintf(stderr,"%s = %i\n", name, *((int *) value));
 | 
|---|
| 1450 |                   //value += sizeof(int);
 | 
|---|
| 1451 |                   break;
 | 
|---|
| 1452 |                 default:
 | 
|---|
| 1453 |                 case(string_type):
 | 
|---|
| 1454 |                   if (value != NULL) {
 | 
|---|
| 1455 |                     //if (maxlength == -1) maxlength = strlen((char *)value); // get maximum size of string array
 | 
|---|
| 1456 |                     maxlength = MAXSTRINGSIZE;
 | 
|---|
| 1457 |                     length = maxlength > (dummy-dummy1) ? (dummy-dummy1) : maxlength; // cap at maximum
 | 
|---|
| 1458 |                     strncpy((char *)value, dummy1, length);  // copy as much
 | 
|---|
| 1459 |                     ((char *)value)[length] = '\0';  // and set end marker
 | 
|---|
| 1460 |                     if ((verbose) && (i == xth-1)) fprintf(stderr,"%s is '%s' (%i chars)\n",name,((char *) value), length);
 | 
|---|
| 1461 |                     //value += sizeof(char);
 | 
|---|
| 1462 |                   } else {
 | 
|---|
| 1463 |                   }
 | 
|---|
| 1464 |                 break;
 | 
|---|
| 1465 |               }
 | 
|---|
| 1466 |             }
 | 
|---|
| 1467 |             while (*dummy == '\t')
 | 
|---|
| 1468 |               dummy++;
 | 
|---|
| 1469 |           }
 | 
|---|
| 1470 |         }
 | 
|---|
| 1471 |       }
 | 
|---|
| 1472 |     }
 | 
|---|
| 1473 |   } 
 | 
|---|
| 1474 |   if ((type >= row_int) && (verbose)) fprintf(stderr,"\n");
 | 
|---|
| 1475 |   Free((void **)&free_dummy, "config::ParseForParameter: *free_dummy");
 | 
|---|
| 1476 |   if (!sequential) {
 | 
|---|
| 1477 |     file->clear();
 | 
|---|
| 1478 |     file->seekg(file_position, ios::beg);  // rewind to start position
 | 
|---|
| 1479 |   }
 | 
|---|
| 1480 |   //fprintf(stderr, "End of Parsing\n\n");
 | 
|---|
| 1481 |   
 | 
|---|
| 1482 |   return (found); // true if found, false if not
 | 
|---|
| 1483 | }
 | 
|---|