Changes in / [848729:dafe43]


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9 edited

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  • molecuilder/src/analyzer.cpp

    r848729 rdafe43  
    2929  ForceMatrix Shielding;
    3030  ForceMatrix ShieldingPAS;
     31  ForceMatrix Chi;
     32  ForceMatrix ChiPAS;
    3133  EnergyMatrix Time;
    3234  EnergyMatrix EnergyFragments;
    … …  
    3537  ForceMatrix ShieldingFragments;
    3638  ForceMatrix ShieldingPASFragments;
     39  ForceMatrix ChiFragments;
     40  ForceMatrix ChiPASFragments;
    3741  KeySetsContainer KeySet;
    3842  ofstream output;
    … …  
    9094    if (!Shielding.ParseFragmentMatrix(argv[1], dir, ShieldingSuffix, 1, 0)) return 1;
    9195    if (!ShieldingPAS.ParseFragmentMatrix(argv[1], dir, ShieldingPASSuffix, 1, 0)) return 1;
     96    if (!Chi.ParseFragmentMatrix(argv[1], dir, ChiSuffix, 1, 0)) return 1;
     97    if (!ChiPAS.ParseFragmentMatrix(argv[1], dir, ChiPASSuffix, 1, 0)) return 1;
    9298  }
    9399
    … …  
    109115    if(!ShieldingFragments.ParseIndices(argv[1])) return 1;
    110116    if(!ShieldingPASFragments.ParseIndices(argv[1])) return 1;
     117    if(!Chi.ParseIndices(argv[1])) return 1;
     118    if(!ChiPAS.ParseIndices(argv[1])) return 1;
     119    if (!ChiFragments.AllocateMatrix(Chi.Header, Chi.MatrixCounter, Chi.RowCounter, Chi.ColumnCounter)) return 1;
     120    if (!ChiPASFragments.AllocateMatrix(ChiPAS.Header, ChiPAS.MatrixCounter, ChiPAS.RowCounter, ChiPAS.ColumnCounter)) return 1;
     121    if(!ChiFragments.ParseIndices(argv[1])) return 1;
     122    if(!ChiPASFragments.ParseIndices(argv[1])) return 1;
    111123  }
    112124
    … …  
    122134    if (!ShieldingFragments.ParseFragmentMatrix(argv[1], dir, ShieldingFragmentSuffix, 1, 0)) return 1;
    123135    if (!ShieldingPASFragments.ParseFragmentMatrix(argv[1], dir, ShieldingPASFragmentSuffix, 1, 0)) return 1;
     136    if (!ChiFragments.ParseFragmentMatrix(argv[1], dir, ChiFragmentSuffix, 1, 0)) return 1;
     137    if (!ChiPASFragments.ParseFragmentMatrix(argv[1], dir, ChiPASFragmentSuffix, 1, 0)) return 1;
    124138  }
    125139
    … …  
    159173      for(int k=0;k<ShieldingPAS.ColumnCounter;k++)
    160174        output << scientific << ShieldingPAS.Matrix[ ShieldingPAS.MatrixCounter ][j][k] << "\t";
     175      output << endl;
     176    }
     177    output << endl;
     178
     179    output << endl << "Total Chis" << endl << "===============" << endl << Chi.Header[Hessian.MatrixCounter] << endl;
     180    for(int j=0;j<Chi.RowCounter[Chi.MatrixCounter];j++) {
     181      for(int k=0;k<Chi.ColumnCounter[Chi.MatrixCounter];k++)
     182        output << scientific << Chi.Matrix[ Chi.MatrixCounter ][j][k] << "\t";
     183      output << endl;
     184    }
     185    output << endl;
     186 
     187    output << endl << "Total Chis PAS" << endl << "===============" << endl << ChiPAS.Header[ChiPAS.MatrixCounter] << endl;
     188    for(int j=0;j<ChiPAS.RowCounter[ChiPAS.MatrixCounter];j++) {
     189      for(int k=0;k<ChiPAS.ColumnCounter[ChiPAS.MatrixCounter];k++)
     190        output << scientific << ChiPAS.Matrix[ ChiPAS.MatrixCounter ][j][k] << "\t";
    161191      output << endl;
    162192    }
    … …  
    228258      output << endl;
    229259    }
    230   }
    231   output.close();
     260    output.close();
     261    if (!CreateDataDeltaForcesOrderPerAtom(ChiPAS, ChiPASFragments, KeySet, argv[3], "DeltaChisPAS-Order", "Plot of error between approximated Chis and full Chis versus the Bond Order", datum)) return 1;
     262    if (!CreateDataForcesOrderPerAtom(ChiPASFragments, KeySet, argv[3], "ChisPAS-Order", "Plot of approximated Chis versus the Bond Order", datum)) return 1;
     263    if (!AppendOutputFile(output, argv[3], "ChisPAS-Order.dat" )) return false;
     264    output << endl << "# Full" << endl;
     265    for(int j=0;j<ChiPAS.RowCounter[ChiPAS.MatrixCounter];j++) {
     266      output << j << "\t";
     267      for(int k=0;k<ChiPAS.ColumnCounter[ChiPAS.MatrixCounter];k++)
     268        output << scientific <<  ChiPAS.Matrix[ ChiPAS.MatrixCounter ][j][k] << "\t"; //*(((k>1) && (k<6))? 1.e6 : 1.) << "\t";
     269      output << endl;
     270    }
     271    output.close();
     272  }
    232273
    233274 
    … …  
    404445    }
    405446    output << "'ShieldingsPAS-Order.dat' index " << KeySet.Order << " title 'Full' using ($1+" << step*(double)KeySet.Order << "):7 with boxes" << endl;
     447    output.close(); 
     448    output2.close(); 
     449
     450    if(!OpenOutputFile(output, argv[3], "ChisPAS-Order.pyx")) return 1;
     451    if(!OpenOutputFile(output2, argv[3], "DeltaChisPAS-Order.pyx")) return 1;
     452    CreatePlotHeader(output, "ChisPAS-Order", 1, "top right", NULL, NULL,  1, 5, "nuclei index", "iso chemical Chi value [ppm]");
     453    CreatePlotHeader(output2, "DeltaChisPAS-Order", 1, "top right", NULL, NULL,  1, 5, "nuclei index", "iso chemical Chi value [ppm]");
     454    output << "set boxwidth " << step << endl;
     455    output << "plot [0:" << ChiPAS.RowCounter[ChiPAS.MatrixCounter]+10 << "]\\" << endl;
     456    output2 << "plot [0:" << ChiPAS.RowCounter[ChiPAS.MatrixCounter]+10 << "]\\" << endl;
     457    for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
     458      output << "'ChisPAS-Order.dat' index " << BondOrder << " title 'Order " << BondOrder+1 << "' using ($1+" << step*(double)BondOrder << "):7 with boxes, \\" << endl;
     459      output2 << "'DeltaChisPAS-Order.dat' index " << BondOrder << " title 'Order " << BondOrder+1 << "' using ($1):7 with linespoints";
     460      if (BondOrder-1 != KeySet.Order)
     461        output2 << ", \\" << endl;
     462    }
     463    output << "'ChisPAS-Order.dat' index " << KeySet.Order << " title 'Full' using ($1+" << step*(double)KeySet.Order << "):7 with boxes" << endl;
    406464    output.close(); 
    407465    output2.close(); 

  • molecuilder/src/joiner.cpp

    r848729 rdafe43  
    2828  ForceMatrix ShieldingFragments;
    2929  ForceMatrix ShieldingPASFragments;
     30  EnergyMatrix Chi;
     31  EnergyMatrix ChiPAS;
     32  EnergyMatrix ChiFragments;
     33  EnergyMatrix ChiPASFragments;
    3034  KeySetsContainer KeySet; 
    3135  stringstream prefix;
    … …  
    6670    if (!Shielding.ParseFragmentMatrix(argv[1], dir, ShieldingSuffix, 1, 0)) return 1;
    6771    if (!ShieldingPAS.ParseFragmentMatrix(argv[1], dir, ShieldingPASSuffix, 1, 0)) return 1;
     72    if (!Chi.ParseFragmentMatrix(argv[1], dir, ChiSuffix, 1, 0)) return 1;
     73    if (!ChiPAS.ParseFragmentMatrix(argv[1], dir, ChiPASSuffix, 1, 0)) return 1;
    6874  }
    6975
    … …  
    7985    if(!Shielding.ParseIndices(argv[1])) return 1;
    8086    if(!ShieldingPAS.ParseIndices(argv[1])) return 1;
     87    if(!Chi.ParseIndices(argv[1])) return 1;
     88    if(!ChiPAS.ParseIndices(argv[1])) return 1;
    8189  }
    8290
    8391  // ---------- Parse the KeySets into an array ---------------
    8492  if (!KeySet.ParseKeySets(argv[1], Force.RowCounter, Force.MatrixCounter)) return 1;
    85 
    8693  if (!KeySet.ParseManyBodyTerms()) return 1;
     94
    8795  if (!EnergyFragments.AllocateMatrix(Energy.Header, Energy.MatrixCounter, Energy.RowCounter, Energy.ColumnCounter)) return 1;
    8896  if (Hcorrected)  HcorrectionFragments.AllocateMatrix(Hcorrection.Header, Hcorrection.MatrixCounter, Hcorrection.RowCounter, Hcorrection.ColumnCounter);
    … …  
    9199    if (!ShieldingFragments.AllocateMatrix(Shielding.Header, Shielding.MatrixCounter, Shielding.RowCounter, Shielding.ColumnCounter)) return 1;
    92100    if (!ShieldingPASFragments.AllocateMatrix(ShieldingPAS.Header, ShieldingPAS.MatrixCounter, ShieldingPAS.RowCounter, ShieldingPAS.ColumnCounter)) return 1;
     101    if (!ChiFragments.AllocateMatrix(Chi.Header, Chi.MatrixCounter, Chi.RowCounter, Chi.ColumnCounter)) return 1;
     102    if (!ChiPASFragments.AllocateMatrix(ChiPAS.Header, ChiPAS.MatrixCounter, ChiPAS.RowCounter, ChiPAS.ColumnCounter)) return 1;
    93103  }
    94104 
    … …  
    99109    if(!Shielding.SetLastMatrix(0., 2)) return 1;
    100110    if(!ShieldingPAS.SetLastMatrix(0., 2)) return 1;
     111    if(!Chi.SetLastMatrix(0., 2)) return 1;
     112    if(!ChiPAS.SetLastMatrix(0., 2)) return 1;
    101113  }
    102114
    … …  
    119131    if (!Force.SumSubForces(ForceFragments, KeySet, BondOrder, 1.)) return 1;
    120132    if (periode != NULL) { // also look for PAS values
    121       cout << "Summing shieldings of order " << BondOrder+1 << " ..." << endl;
     133      cout << "Summing shieldings and susceptibilities of order " << BondOrder+1 << " ..." << endl;
    122134      if (!ShieldingFragments.SumSubManyBodyTerms(Shielding, KeySet, BondOrder)) return 1;
    123135      if (!Shielding.SumSubForces(ShieldingFragments, KeySet, BondOrder, 1.)) return 1;
    124136      if (!ShieldingPASFragments.SumSubManyBodyTerms(ShieldingPAS, KeySet, BondOrder)) return 1;
    125137      if (!ShieldingPAS.SumSubForces(ShieldingPASFragments, KeySet, BondOrder, 1.)) return 1;
     138      if (!ChiFragments.SumSubManyBodyTerms(Chi, KeySet, BondOrder)) return 1;
     139      if (!Chi.SumSubForces(ChiFragments, KeySet, BondOrder, 1.)) return 1;
     140      if (!ChiPASFragments.SumSubManyBodyTerms(ChiPAS, KeySet, BondOrder)) return 1;
     141      if (!ChiPAS.SumSubForces(ChiPASFragments, KeySet, BondOrder, 1.)) return 1;
    126142    }
    127143
    … …  
    138154      if (!Shielding.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ShieldingSuffix)) return 1;
    139155      if (!ShieldingPAS.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ShieldingPASSuffix)) return 1;
     156      if (!Chi.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ChiSuffix)) return 1;
     157      if (!ChiPAS.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ChiPASSuffix)) return 1;
    140158    }
    141159  }
    … …  
    160178    prefix << dir << ShieldingPASFragmentSuffix;
    161179    if (!ShieldingPASFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
     180    prefix.str(" ");
     181    prefix << dir << ChiFragmentSuffix;
     182    if (!ChiFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
     183    prefix.str(" ");
     184    prefix << dir << ChiPASFragmentSuffix;
     185    if (!ChiPASFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
    162186  }
    163187
    … …  
    169193    if (!Shielding.WriteLastMatrix(argv[1], dir, ShieldingFragmentSuffix)) return 1;
    170194    if (!ShieldingPAS.WriteLastMatrix(argv[1], dir, ShieldingPASFragmentSuffix)) return 1;
     195    if (!Chi.WriteLastMatrix(argv[1], dir, ChiFragmentSuffix)) return 1;
     196    if (!ChiPAS.WriteLastMatrix(argv[1], dir, ChiPASFragmentSuffix)) return 1;
    171197  }
    172198

  • molecuilder/src/parser.hpp

    r848729 rdafe43  
    2525#define ShieldingFragmentSuffix ".sigma_all_fragment.all"
    2626#define ShieldingPASFragmentSuffix ".sigma_all_PAS_fragment.all"
     27#define ChiSuffix ".chi_all.csv"
     28#define ChiPASSuffix ".chi_all_PAS.csv"
     29#define ChiFragmentSuffix ".chi_all_fragment.all"
     30#define ChiPASFragmentSuffix ".chi_all_PAS_fragment.all"
    2731#define TimeSuffix ".speed"
    2832#define EnergyFragmentSuffix ".energyfragment.all"

  • util/src/AdaptiveANOVA.sh.in

    r848729 rdafe43  
    33# Performs an adaptive simulation with molecuilder
    44
    5 exec_prefix=@prefix@
     5exec_prefix="/mount/bespin/heber/workspace/ESPACK/bin/"
    66MOLECUILDER="$exec_prefix/molecuilder"
    77JOINER="$exec_prefix/joiner"

  • util/src/CalculateDensity.sh.in

    r848729 rdafe43  
    33# calculates the density of a molecule contained in a espack config file
    44
    5 MOLECUILDER="@bindir@/molecuilder"
     5MOLECUILDER="/home/heber/workspace/ESPACK/bin/molecuilder"
    66
    77if [ -z $1 ]; then

  • util/src/CalculateMass.sh.in

    r848729 rdafe43  
    33# calculates mass of a molecule in a XYZ file
    44
    5 ELEMENTSDB="@bindir@/elements.db"
     5ELEMENTSDB="/home/heber/workspace/ESPACK/bin/elements.db"
    66
    77if [ -z "$1" ]; then

  • util/src/CreateFromXYZ.sh.in

    r848729 rdafe43  
    1111exec_prefix=@prefix@
    1212molecuilder=@bindir@
    13 pseudopot="${exec_prefix}/../pcp/pseudopot"
     13pseudopot="${exec_prefix}/defaults/pseudopot"
    1414
    1515echo "Target dir is ${pfad}, using xyz file ${mol}."

  • util/src/SortByRings.sh.in

    r848729 rdafe43  
    5050lines=(`cat <$file`)
    5151map=(`cat <MoleculesRingSorted.dat`)
    52 i=1
    53 echo "${lines[0]}" >>${file}_sorted
     52i=0
    5453while [ $i -lt ${#lines[@]} ]; do
     54        let j=`echo ${map[$i]}  | awk -F" " {'print $1'}`
    5555        #echo "lines: ${lines[$i]}"
    5656        #echo "Map: ${map[$i]} -> $i"
    57         let j=`echo ${map[$i]}  | awk -F" " {'print $1'}`
    58         name=`echo "${lines[$j]}" | awk -F" " {'print $2'}`
    59         echo -e -n "$i\t$name\t" >> ${file}_sorted
    60         echo "${lines[$j]}" | sed -e "s#[0-9]*\t[0-9a-zA-Z,_\-]*\t##" >>${file}_sorted
     57        name=`echo "${lines[$j]}" | awk -F" " {'print $1'}`
     58        echo -e -n "$name\t$i\t" >> ${file}_sorted
     59        echo "${lines[$j]}" | sed -e "s#[0-9a-zA-Z,_\-]*\t[0-9]*\t##" >>${file}_sorted
    6160        let i=$i+1
    6261done

  • util/src/dynamicANOVA.sh.in

    r848729 rdafe43  
    125125        cpus=`cat /proc/cpuinfo | grep processor | wc -l`
    126126        echo "localhost" >$PBS_NODEFILE
    127         while [ $i -lt $cpus ]; do      # add one localhost per cpu to machines file
     127        while [ $i -lt $cpus ]; do      # add one localhost per cpu to machines file
    128128                echo "localhost" >>$PBS_NODEFILE
    129129                let i=$i+1
    … …  
    243243  done
    244244
    245         # go through all groups and run the job
    246         olddivisor=$divisor
    247         if [ $divisor -gt $frag ]; then
    248           divisor=$frag
     245  # go through all groups and run the job
     246  olddivisor=$divisor
     247  if [ $divisor -gt $frag ]; then
     248        divisor=$frag
    249249  fi
    250250  grp=0;
    … …  
    256256    let grp=$grp+1
    257257        done
    258   divisor=$olddivisor
     258        divisor=$olddivisor     
    259259
    260260# wait till all ProcRuns files are gone
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