Gaussian checkpoint writer

include/votca/xtp/aobasis.h

@@ -53,6 +53,14 @@ class AOBasis {
 
   Index getNumofShells() const { return Index(_aoshells.size()); }
 
+  Index getNumberOfPrimitives() const {
+    Index totalPrimitives = 0;
+    for (const AOShell& shell : _aoshells) {
+      totalPrimitives += shell.getSize();
+    }
+    return totalPrimitives;
+  }
+
   Index getMaxNprim() const;
 
   Index getMaxL() const;

include/votca/xtp/gaussianwriter.h

@@ -0,0 +1,51 @@
+/*
+ *            Copyright 2009-2020 The VOTCA Development Team
+ *                       (http://www.votca.org)
+ *
+ *      Licensed under the Apache License, Version 2.0 (the "License")
+ *
+ * You may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *              http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+#pragma once
+#ifndef VOTCA_XTP_GAUSSIANWRITER_H
+#define VOTCA_XTP_GAUSSIANWRITER_H
+
+// Local VOTCA includes
+#include "votca/xtp/logger.h"
+#include "votca/xtp/orbitals.h"
+#include "votca/xtp/orbreorder.h"
+#include "votca/xtp/qmtool.h"
+#include <fstream>
+
+namespace votca {
+namespace xtp {
+class GaussianWriter {
+ public:
+  GaussianWriter(Logger& log) : _log(log){};
+
+  ~GaussianWriter() = default;
+
+  void WriteFile(const std::string& filename, const Orbitals& orbitals) const;
+
+ private:
+  Logger& _log;
+  Index toGaussianL(L l) const;
+  std::string reorderedMOCoefficients(const Orbitals& orbitals) const;
+  std::string densityMatrixToString(const Orbitals& orbitals) const;
+};
+
+}  // namespace xtp
+}  // namespace votca
+
+#endif

share/xtp/xml/orb2fchk.xml

@@ -0,0 +1,5 @@
+<?xml version="1.0"?>
+<options>
+  <orb2fchk help="Converts orb files to gaussian fchk files.">
+  </orb2fchk>
+</options>

src/libxtp/factories/toolfactory.cc

@@ -30,6 +30,7 @@
 #include "tools/log2mps.h"
 #include "tools/mol2orb.h"
 #include "tools/molpol.h"
+#include "tools/orb2fchk.h"
 #include "tools/orb2mol.h"
 #include "tools/partialcharges.h"
 #include "tools/qmsandbox.h"
@@ -53,6 +54,7 @@ void QMToolFactory::RegisterAll(void) {
   QMTools().Register<APDFT>("apdft");
   QMTools().Register<Mol2Orb>("mol2orb");
   QMTools().Register<Orb2Mol>("orb2mol");
+  QMTools().Register<Orb2Fchk>("orb2fchk");
 }
 
 }  // namespace xtp

src/libxtp/gaussianwriter.cc

@@ -0,0 +1,307 @@
+#include "votca/xtp/gaussianwriter.h"
+#include "votca/xtp/basisset.h"
+#include <boost/algorithm/string.hpp>
+#include <boost/format.hpp>
+#include <sstream>
+#include <votca/tools/eigenio_matrixmarket.h>
+
+namespace votca {
+namespace xtp {
+
+/*
+ * This function converts VOTCA's L enum to the gaussian equivalent.
+ * Gaussian uses a minus sign to indicate spherical shells.
+ */
+Index GaussianWriter::toGaussianL(L l) const {
+  switch (l) {
+    case L::S:
+      return 0;
+    case L::P:
+      return 1;
+    default:
+      return -1 * static_cast<Index>(l);
+  }
+}
+
+std::string GaussianWriter::reorderedMOCoefficients(
+    const Orbitals& orbitals) const {
+  // Setup the reordering parameters
+  std::array<Index, 49> multipliers;
+  multipliers.fill(-1);
+  // clang-format off
+  // the ordering of the m quantumnumbers for every shell in gaussian
+  std::array<Index, 49> gaussianOrder={{
+            0, //s
+            1,-1,0, //p
+            0,1,-1,2,-2, //d
+            0,1,-1,2,-2,3,-3, //f 
+            0,1,-1,2,-2,3,-3,4,-4, //g
+            0,1,-1,2,-2,3,-3,4,-4,5,-5, // h
+            0,1,-1,2,-2,3,-3,4,-4,5,-5,6,-6 // i
+  }};
+  // clang-format on
+  OrbReorder reorder(gaussianOrder, multipliers, true);
+  Eigen::MatrixXd moCoefficients = orbitals.MOs().eigenvectors();
+  reorder.reorderOrbitals(moCoefficients, orbitals.SetupDftBasis());
+
+  // put the reordered mos in a string
+  std::stringstream mos_string;
+
+  int temp_int = 1;
+  for (Index i = 0; i < moCoefficients.rows(); ++i) {
+    for (Index j = 0; j < moCoefficients.cols(); ++j) {
+      mos_string << boost::format("%16.8e") % moCoefficients(j, i);
+      if (temp_int % 5 == 0) {
+        mos_string << "\n";
+      }
+      temp_int++;
+    }
+  }
+  mos_string << ((temp_int - 1) % 5 == 0 ? "" : "\n");
+
+  return mos_string.str();
+}
+
+std::string GaussianWriter::densityMatrixToString(
+    const Orbitals& orbitals) const {
+
+  // Setup the reordering parameters
+  std::array<Index, 49> multipliers;
+  multipliers.fill(-1);
+  // clang-format off
+  // the ordering of the m quantumnumbers for every shell in gaussian
+  std::array<Index, 49> gaussianOrder={{
+            0, //s
+            1,-1,0, //p
+            0,1,-1,2,-2, //d
+            0,1,-1,2,-2,3,-3, //f 
+            0,1,-1,2,-2,3,-3,4,-4, //g
+            0,1,-1,2,-2,3,-3,4,-4,5,-5, // h
+            0,1,-1,2,-2,3,-3,4,-4,5,-5,6,-6 // i
+  }};
+  // clang-format on
+  OrbReorder reorder(gaussianOrder, multipliers, true);
+  Eigen::MatrixXd density = orbitals.DensityMatrixGroundState();
+  reorder.reorderOperator(density, orbitals.SetupDftBasis());
+
+  votca::tools::EigenIO_MatrixMarket::WriteMatrix("density.mm", density);
+
+  // put the reordered mos in a string
+  std::stringstream density_string;
+
+  int temp_int = 1;
+
+  for (Index i = 0; i < density.rows(); ++i) {
+    for (Index j = 0; j <= i; ++j) {
+      density_string << boost::format("%16.8e") % density(i, j);
+      if (temp_int % 5 == 0) {
+        density_string << "\n";
+      }
+      temp_int++;
+    }
+  }
+  density_string << ((temp_int - 1) % 5 == 0 ? "" : "\n");
+
+  return density_string.str();
+}
+
+void GaussianWriter::WriteFile(const std::string& basename,
+                               const Orbitals& orbitals) const {
+  if (!orbitals.hasDFTbasisName()) {
+    throw std::runtime_error(".orb file does not contain a basisset name");
+  }
+
+  AOBasis basis = orbitals.SetupDftBasis();
+
+  std::ofstream outFile(basename + ".fchk");
+  if (outFile.is_open()) {
+    int temp_int;
+    // job description
+    outFile << basename << ", fchk created by VOTCA-XTP\n";
+    outFile << "DUMMY_TYPE    DUMMY_METHOD    " << orbitals.getDFTbasisName()
+            << "\n";
+
+    // clang-format off
+    outFile << boost::format("%-43s%-2s%15d\n") % "number of atoms" % "I" % orbitals.QMAtoms().size();
+    outFile << boost::format("%-43s%-2s%15d\n") % "Charge" % "I" % 0;
+    outFile << boost::format("%-43s%-2s%15d\n") % "Multiplicity" % "I" % 1;
+    outFile << boost::format("%-43s%-2s%15d\n") % "Number of electrons" % "I" % (2*orbitals.getNumberOfAlphaElectrons());
+    outFile << boost::format("%-43s%-2s%15d\n") % "Number of alpha electrons" % "I" % orbitals.getNumberOfAlphaElectrons();
+    outFile << boost::format("%-43s%-2s%15d\n") % "Number of beta electrons" % "I" % orbitals.getNumberOfAlphaElectrons();
+    outFile << boost::format("%-43s%-2s%15d\n") % "Number of basis functions" % "I" % basis.AOBasisSize();
+    outFile << boost::format("%-43s%-2s%15d\n") % "Number of independent functions" % "I" % basis.AOBasisSize();
+    // clang-format on
+    // ATOMIC NUMBERS
+    outFile << boost::format("%-43s%-2s N=  %10d\n") % "Atomic numbers" % "I" %
+                   orbitals.QMAtoms().size();
+    temp_int = 1;
+    for (const auto& atom : orbitals.QMAtoms()) {
+      outFile << boost::format("%12d") % atom.getElementNumber();
+      if (temp_int % 6 == 0) {
+        outFile << "\n";
+      }
+      temp_int++;
+    }
+    outFile << ((temp_int - 1) % 6 == 0 ? "" : "\n");
+    // NUCLEAR CHARGES
+    outFile << boost::format("%-43s%-2s N=  %10d\n") % "Nuclear charges" % "R" %
+                   orbitals.QMAtoms().size();
+    temp_int = 1;
+    for (const auto& atom : orbitals.QMAtoms()) {
+      outFile << boost::format("%16.8e") % (double)atom.getNuccharge();
+      if (temp_int % 5 == 0) {
+        outFile << "\n";
+      }
+      temp_int++;
+    }
+    outFile << ((temp_int - 1) % 5 == 0 ? "" : "\n");
+    // CURRENT CARTESIAN COORDINATES
+    outFile << boost::format("%-43s%-2s N=  %10d\n") %
+                   "Current cartesian coordinates" % "R" %
+                   (3 * orbitals.QMAtoms().size());
+    temp_int = 1;
+    for (const auto& atom : orbitals.QMAtoms()) {
+      for (int i = 0; i < 3; ++i) {
+        outFile << boost::format("%16.8e") % atom.getPos()(i);
+        if (temp_int % 5 == 0) {
+          outFile << "\n";
+        }
+        temp_int++;
+      }
+    }
+    outFile << ((temp_int - 1) % 5 == 0 ? "" : "\n");
+    // NUMBER OF PRIMITIVE SHELLS
+    outFile << boost::format("%-43s%-2s%15d\n") % "Number of primitive shells" %
+                   "I" % basis.getNumberOfPrimitives();
+    // NUMBER OF CONTRACTED SHELLS
+    outFile << boost::format("%-43s%-2s%15d\n") %
+                   "Number of contracted shells" % "I" % basis.getNumofShells();
+    // PURE/CARTESIAN D
+    outFile << boost::format("%-43s%-2s%15d\n") % "Pure/Cartesian d shells " %
+                   "I" % 0;
+    // PURE/CARTESIAN F
+    outFile << boost::format("%-43s%-2s%15d\n") % "Pure/Cartesian f shells " %
+                   "I" % 0;
+    // HIGHEST ANGULAR MOMENTUM
+    outFile << boost::format("%-43s%-2s%15d\n") % "Highest angular momentum " %
+                   "I" % basis.getMaxL();
+    // HIGHEST ANGULAR MOMENTUM
+    outFile << boost::format("%-43s%-2s%15d\n") %
+                   "Largest degree of contraction " % "I" % basis.getMaxNprim();
+    // SHELL TYPES
+    outFile << boost::format("%-43s%-2s N=  %10d\n") % "Shell types" % "I" %
+                   (basis.getNumofShells());
+    temp_int = 1;
+    for (const auto& shell : basis) {
+      outFile << boost::format("%12d") % toGaussianL(shell.getL());
+      if (temp_int % 6 == 0) {
+        outFile << "\n";
+      }
+      temp_int++;
+    }
+    outFile << ((temp_int - 1) % 6 == 0 ? "" : "\n");
+    // NR OF PRIMITIVES PER SHELL
+    outFile << boost::format("%-43s%-2s N=  %10d\n") %
+                   "Number of primitives per shell" % "I" %
+                   (basis.getNumofShells());
+    temp_int = 1;
+    for (const AOShell& shell : basis) {
+      outFile << boost::format("%12d") % shell.getSize();
+      if (temp_int % 6 == 0) {
+        outFile << "\n";
+      }
+      temp_int++;
+    }
+    outFile << ((temp_int - 1) % 6 == 0 ? "" : "\n");
+    // SHELL TO ATOM MAP
+    outFile << boost::format("%-43s%-2s N=  %10d\n") % "Shell to atom map" %
+                   "I" % (basis.getNumofShells());
+    temp_int = 1;
+    for (const AOShell& shell : basis) {
+      // Gaussian indices start at 1, hence the + 1
+      outFile << boost::format("%12d") % (shell.getAtomIndex() + 1);
+      if (temp_int % 6 == 0) {
+        outFile << "\n";
+      }
+      temp_int++;
+    }
+    outFile << ((temp_int - 1) % 6 == 0 ? "" : "\n");
+    // PRIMITIVE EXPONENTS
+    outFile << boost::format("%-43s%-2s N=  %10d\n") % "Primitive exponents" %
+                   "R" % basis.getNumberOfPrimitives();
+    temp_int = 1;
+    for (const AOShell& shell : basis) {
+      for (const AOGaussianPrimitive& prim : shell) {
+        outFile << boost::format("%16.8e") % prim.getDecay();
+        if (temp_int % 5 == 0) {
+          outFile << "\n";
+        }
+        temp_int++;
+      }
+    }
+    outFile << ((temp_int - 1) % 5 == 0 ? "" : "\n");
+    // CONTRACTION COEFFICIENTS
+    outFile << boost::format("%-43s%-2s N=  %10d\n") %
+                   "Contraction coefficients" % "R" %
+                   basis.getNumberOfPrimitives();
+    temp_int = 1;
+    for (const AOShell& shell : basis) {
+      for (const AOGaussianPrimitive& prim : shell) {
+        outFile << boost::format("%16.8e") % prim.getContraction();
+        if (temp_int % 5 == 0) {
+          outFile << "\n";
+        }
+        temp_int++;
+      }
+    }
+    outFile << ((temp_int - 1) % 5 == 0 ? "" : "\n");
+    // SHELL COORDINATES
+    outFile << boost::format("%-43s%-2s N=  %10d\n") %
+                   "Coordinates of each shell" % "R" %
+                   (3 * basis.getNumofShells());
+    temp_int = 1;
+    for (const AOShell& shell : basis) {
+      for (int i = 0; i < 3; ++i) {
+        outFile << boost::format("%16.8e") % shell.getPos()(i);
+        if (temp_int % 5 == 0) {
+          outFile << "\n";
+        }
+        temp_int++;
+      }
+    }
+    outFile << ((temp_int - 1) % 5 == 0 ? "" : "\n");
+    // TOTAL ENERGY
+    outFile << boost::format("%-43s%-2s%22.15e\n") % "Total Energy" % "R" %
+                   orbitals.getDFTTotalEnergy();
+    // ALPHA ORBITAL ENERGIES
+    outFile << boost::format("%-43s%-2s N=  %10d\n") %
+                   "Alpha Orbital Energies" % "R" %
+                   orbitals.MOs().eigenvalues().size();
+    temp_int = 1;
+    for (Index i = 0; i < orbitals.MOs().eigenvalues().size(); ++i) {
+      outFile << boost::format("%16.8e") % orbitals.MOs().eigenvalues()[i];
+      if (temp_int % 5 == 0) {
+        outFile << "\n";
+      }
+      temp_int++;
+    }
+    outFile << ((temp_int - 1) % 5 == 0 ? "" : "\n");
+    // ALPHA ORBITAL ENERGIES
+    outFile << boost::format("%-43s%-2s N=  %10d\n") % "Alpha MO coefficients" %
+                   "R" %
+                   (orbitals.MOs().eigenvalues().size() *
+                    orbitals.MOs().eigenvalues().size());
+    outFile << reorderedMOCoefficients(orbitals);
+    // DENSITY MATRIX
+    outFile << boost::format("%-43s%-2s N=  %10d\n") % "Total SCF Density" %
+                   "R" %
+                   ((orbitals.MOs().eigenvalues().size() *
+                     (orbitals.MOs().eigenvalues().size() - 1)) /
+                        2 +
+                    orbitals.MOs().eigenvalues().size());
+    outFile << densityMatrixToString(orbitals);
+  }
+}
+
+}  // namespace xtp
+}  // namespace votca