initial commit

Makefile

@@ -0,0 +1,113 @@
+#CXX=icpc -openmp -O3 
+#cc=icc -openmp -O3
+CXX=g++ -O3 -g
+cc=gcc -O3 -g
+#CXX=g++ -O3 -g  
+
+spg_incs = spgstuff/arithmetic.h \
+           spgstuff/delaunay.h \
+           spgstuff/kpoint.h \
+           spgstuff/pointgroup.h \
+           spgstuff/sitesym_database.h \
+           spgstuff/spg_database.h \
+           spgstuff/symmetry.h \
+           spgstuff/cell.h \
+           spgstuff/hall_symbol.h \
+           spgstuff/mathfunc.h \
+           spgstuff/primitive.h \
+           spgstuff/site_symmetry.h \
+           spgstuff/spglib.h \
+           spgstuff/tetrahedron_method.h \
+           spgstuff/debug.h \
+           spgstuff/kgrid.h \
+           spgstuff/niggli.h \
+           spgstuff/refinement.h \
+           spgstuff/spacegroup.h \
+           spgstuff/spin.h \
+           spgstuff/version.h
+spg_o = spgstuff/arithmetic.o \
+        spgstuff/cell.o \
+        spgstuff/debug.o \
+        spgstuff/delaunay.o \
+        spgstuff/hall_symbol.o \
+        spgstuff/kgrid.o \
+        spgstuff/kpoint.o \
+        spgstuff/mathfunc.o \
+        spgstuff/niggli.o \
+        spgstuff/pointgroup.o \
+        spgstuff/primitive.o \
+        spgstuff/refinement.o \
+        spgstuff/site_symmetry.o \
+        spgstuff/sitesym_database.o \
+        spgstuff/spacegroup.o \
+        spgstuff/spg_database.o \
+        spgstuff/spglib.o \
+        spgstuff/spin.o \
+        spgstuff/symmetry.o \
+        spgstuff/spglib_f.o \
+        spgstuff/tetrahedron_method.o
+
+all:main
+main: main.o pwscfData.o types.o util.o spgstuff/libmyspg.a handleTilemats.o
+	$(CXX) -o main main.o pwscfData.o types.o util.o handleTilemats.o spgstuff/libmyspg.a
+pwscfData.o: pwscfData.cpp pwscfData.h
+	$(CXX) -c pwscfData.cpp
+handleTilemats.o: handleTilemats.cpp handleTilemats.h util.h types.h pwscfData.h
+	$(CXX) -c handleTilemats.cpp
+main.o: main.cpp pwscfData.h handleTilemats.h handlePwscf.h
+	$(CXX) -c main.cpp
+types.o: types.cpp util.h util.h spgstuff/spglib.h
+	$(CXX) -Ispgstuff/ -c types.cpp
+util.o: util.cpp util.h types.h
+	$(CXX) -c util.cpp
+spgstuff/libmyspg.a: $(spg_o) $(spg_incs)
+	ar rcs spgstuff/libmyspg.a $(spg_o)
+clean:
+	rm -f main *.o spgstuff/*.o spgstuff/libmyspg.a 
+
+
+spgstuff/arithmetic.o: spgstuff/arithmetic.c $(spg_incs)
+	$(cc) -o spgstuff/arithmetic.o -c spgstuff/arithmetic.c
+spgstuff/hall_symbol.o: spgstuff/hall_symbol.c $(spg_incs)
+	$(cc) -o spgstuff/hall_symbol.o -c spgstuff/hall_symbol.c
+spgstuff/niggli.o: spgstuff/niggli.c $(spg_incs)
+	$(cc) -o spgstuff/niggli.o -c spgstuff/niggli.c
+spgstuff/sitesym_database.o: spgstuff/sitesym_database.c $(spg_incs)
+	$(cc) -o spgstuff/sitesym_database.o -c spgstuff/sitesym_database.c
+spgstuff/spglib.o: spgstuff/spglib.c $(spg_incs)
+	$(cc) -o spgstuff/spglib.o -c spgstuff/spglib.c
+spgstuff/test.o: spgstuff/test.c $(spg_incs)
+	$(cc) -o spgstuff/test.o -c spgstuff/test.c
+spgstuff/cell.o: spgstuff/cell.c $(spg_incs)
+	$(cc) -o spgstuff/cell.o -c spgstuff/cell.c
+spgstuff/kgrid.o: spgstuff/kgrid.c $(spg_incs)
+	$(cc) -o spgstuff/kgrid.o -c spgstuff/kgrid.c
+spgstuff/pointgroup.o: spgstuff/pointgroup.c $(spg_incs)
+	$(cc) -o spgstuff/pointgroup.o -c spgstuff/pointgroup.c
+spgstuff/site_symmetry.o: spgstuff/site_symmetry.c $(spg_incs)
+	$(cc) -o spgstuff/site_symmetry.o -c spgstuff/site_symmetry.c
+spgstuff/spglib_f.o: spgstuff/spglib_f.c $(spg_incs)
+	$(cc) -o spgstuff/spglib_f.o -c spgstuff/spglib_f.c
+spgstuff/tetrahedron_method.o: spgstuff/tetrahedron_method.c $(spg_incs)
+	$(cc) -o spgstuff/tetrahedron_method.o -c spgstuff/tetrahedron_method.c
+spgstuff/debug.o: spgstuff/debug.c $(spg_incs)
+	$(cc) -o spgstuff/debug.o -c spgstuff/debug.c
+spgstuff/kpoint.o: spgstuff/kpoint.c $(spg_incs)
+	$(cc) -o spgstuff/kpoint.o -c spgstuff/kpoint.c
+spgstuff/primitive.o: spgstuff/primitive.c $(spg_incs)
+	$(cc) -o spgstuff/primitive.o -c spgstuff/primitive.c
+spgstuff/spacegroup.o: spgstuff/spacegroup.c $(spg_incs)
+	$(cc) -o spgstuff/spacegroup.o -c spgstuff/spacegroup.c
+spgstuff/spin.o: spgstuff/spin.c $(spg_incs)
+	$(cc) -o spgstuff/spin.o -c spgstuff/spin.c
+spgstuff/delaunay.o: spgstuff/delaunay.c $(spg_incs)
+	$(cc) -o spgstuff/delaunay.o -c spgstuff/delaunay.c
+spgstuff/mathfunc.o: spgstuff/mathfunc.c $(spg_incs)
+	$(cc) -o spgstuff/mathfunc.o -c spgstuff/mathfunc.c
+spgstuff/refinement.o: spgstuff/refinement.c $(spg_incs)
+	$(cc) -o spgstuff/refinement.o -c spgstuff/refinement.c
+spgstuff/spg_database.o: spgstuff/spg_database.c $(spg_incs)
+	$(cc) -o spgstuff/spg_database.o -c spgstuff/spg_database.c
+spgstuff/symmetry.o: spgstuff/symmetry.c $(spg_incs)
+	$(cc) -o spgstuff/symmetry.o -c spgstuff/symmetry.c
+

NOTES

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+We would like to be able to do the following:
+   1. specify things directly on the command line like before
+   2. read xml snippets and then override their values
+      2A For example: --dmcblock dmc.xml --dmctstep 0.01
+      2B Think about format for jastrows.  Probably do the following: --onebodyjastrowblock Be Beonebody.xml.
+         There is a difficulty with how to addess those parameters though: Probably stick with only being able
+	 to globally change jastrow parameters.
+      2C In order to do this, we will need to be able to hand xmlNodes to the various constructors.
+         Be careful here about memory leaks!!!
+   3. point the code to where an optimization was done and then have it use that determine the "optimal" wavefunction
+   4. With regards to how the code is set up to generate qmcpack input files, probably best to just have
+      an option like --qmcinputfile and then after all of the options changing things about the particleset,
+      wavefunction and the like, just have it do --qmcaction a b c... where a is the number of the action, b is the
+      type of the action, and then everything in c are options to be handled by the type of action listed in b,
+      and this is terminated by the next qmcaction block
+
+   5. Think about creating a atomlibrary type of xml file
+      <atomlibrary>
+        <atom elementType="Symbol" isAllElectron="yes/no" ppHash="md5sum">
+	  <jastrow type="OneBody" function="Bspline">
+	    <correlation elementType="Symbol" cusp="xxx" size="xxx" rcut="xxx">
+	      <coefficients ....>
+	      </coefficients>
+            </correlation>
+          </jastrow>
+	  <jastrow type="OneBody" function="pade2">
+	    <correlation...>
+	      <coefficients ... >
+	      </coefficients>
+            </correlation>
+          </jastrow>
+	  <jastrow type="eeI" function="polynomial">
+	    <correlation ...>
+	      <coefficients ..>
+	      </coefficients>
+	    </correlation>
+	  </jastrow>
+          <hybrid>
+	    <parameter name="cutoff_radius>xxx</parameter>
+	    <parameter name="spline_radius>xxx</parameter>
+	    <parameter name="spline_npoints>xxx</parameter>
+	    <parameter name="lmax">xxx</parameter>
+	  </hybrid>
+	</atom>
+      </atomlibrary>

handlePwscf.h

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+#ifndef HANDLE_PWSCF_H
+#define HANDLE_PWSCF_H
+#include "handleTilemats.h"
+#include "types.h"
+#include "util.h"
+#include <iostream>
+#include <string>
+#include <sstream>
+#include <cstring>
+#include <fstream>
+#include <cmath>
+#include <iomanip>
+using namespace std;
+
+void genWfn(int argc, char* argv[]) {
+
+  string inFileName = "undef";
+  int ssize;
+  int sskgrid[3];
+  int sskshift[3] = {0, 0, 0};
+
+  // read necessary info from the command line
+  for (int i = 1; i < argc; i++) {
+    if (!strcmp(argv[i],"--infile")) {
+      inFileName= string(argv[i+1]);
+    } else if (!strcmp(argv[i],"--supercellsize")) {
+      ssize = atoi(argv[i+1]);
+    } else if (!strcmp(argv[i],"--sskgrid")) {
+      for (int j = 0; j < 3; j++) {
+	stringstream ss1(argv[i+1+j]);
+	ss1 >> sskgrid[j];
+      }
+      i+=3;
+    } else if (!strcmp(argv[i],"--sskshift")) {
+      for (int j = 0; j < 3; j++) {
+	stringstream ss1(argv[i+1+j]);
+	ss1 >> sskshift[j];
+      }
+      i+=3;
+    }
+  }
+
+  if (inFileName == "undef") {
+    cout << "No pwscf input filename was given" << endl;
+  }
+
+  pwscfString ps(inFileName);
+  pwscfData pd(ps);
+
+  threeThreeMat<int> tilemat = getTilemat(pd, ssize);  
+  physSys primcell(pd.ptv, pd.ionNames, pd.atpos);
+  physSys supercell(primcell, tilemat);
+
+  // These are the weighted supercell k-points;
+  vector<weightedKpt> outks;
+  supercell.getMesh(sskgrid[0], sskgrid[1], sskgrid[2], sskshift[0], sskshift[1], sskshift[2], outks);
+
+  // Now need to find the primitive cell k-points necessary
+  int numCopies = getDet(tilemat);
+  vector<weightedKpt> primks;
+
+  // loop over supercell kpoints
+  for (int i = 0; i < outks.size(); i++) {
+    double weight = outks[i].first;
+    vector<location> locPrimKs;
+    getPrimKpts(primcell, supercell, outks[i].second, locPrimKs, numCopies);
+    // for each found primitive cell kpt, see if it is in primks
+    // if it is add it's weight to the existing one
+    // if it is not, add it and its weight
+    for (int j = 0; j < locPrimKs.size(); j++) {
+      int found = 0;
+      for (int k = 0; k < primks.size(); k++) {
+	if (abs(locPrimKs[j][0] - primks[k].second[0]) < 1e-8 &&
+	    abs(locPrimKs[j][1] - primks[k].second[1]) < 1e-8 &&
+	    abs(locPrimKs[j][2] - primks[k].second[2]) < 1e-8) {
+	  primks[k].first+=weight;
+	  found = 1;
+	  k+= primks.size();
+	}
+      }
+      if (!found) {
+	weightedKpt kp;
+	kp.first = weight;
+	for (int k = 0; k < 3; k++) {
+	  kp.second[k] = locPrimKs[j][k];
+	}
+	primks.push_back(kp);
+      }
+    }
+  }
+
+  // Now outks has the symmetry independent supercell kpoints
+  // primks has the necessary primitive cell kpts to generate outks
+
+  stringstream ss;
+  ss << "K_POINTS {CRYSTAL}" << endl;
+  ss.setf(ios_base::fixed, ios_base::floatfield);
+  ss.precision(8);
+  ss << setw(8) << primks.size() << endl;
+  //  ss << setw(16) << "kx" << setw(16) << "ky" << setw(16) << "kz" << setw(16) << "wt" << endl;
+  for (int i = 0; i < primks.size(); i++) {
+    ss << setw(16) << primks[i].second[0] << setw(16) << primks[i].second[1] << setw(16) << primks[i].second[2] << setw(16) << primks[i].first;
+    if (i+1 < primks.size()) {
+      ss << endl;
+    }
+  }
+  string kpointstring = ss.str();
+
+  // now need to replace the pwscfString (ps) object's K_POINTS card with a new
+  // one using kpointstring  (need a pwscfReplaceWholeCard)
+  // Also need to change the calculation from scf to nscf  (pwscfString.changePwscfToken)
+  // Also need to make sure the output has nosym=.true. and noinv=.true.  (need an addToPwscfSection)
+  ps.changePwscfToken("calculation", "'nscf'");
+  ps.removePwscfToken("nosym");
+  ps.removePwscfToken("noinv");
+  ps.addToPwscfSection("system", "nosym", ".true.");
+  ps.addToPwscfSection("system", "noinv", ".true.");
+  ps.replaceWholePwscfCard("K_POINTS", kpointstring);
+
+  string nscfstring = ps.getOutput();
+
+  stringstream p2xstringss;
+  p2xstringss << "&inputpp" << endl;
+  p2xstringss << "   outdir = '" << pd.outputDir << "'" << endl;
+  p2xstringss << "   prefix = '" << pd.prefix << "'" << endl;
+  p2xstringss << "   write_psir=.false." << endl;
+  p2xstringss << "/" << endl;
+
+
+  string nscfFname = inFileName;
+  // get rid of -scf if file has it
+  size_t index = nscfFname.find("-scf");
+  if (index != string::npos) {
+    nscfFname.erase(index, 4);
+  }
+  // get rid of .in if file has it
+  size_t index2 = nscfFname.find(".in");
+  if (index2 != string::npos) {
+    nscfFname.erase(index2,3);
+  }
+  stringstream fnss;
+  fnss << nscfFname;
+  fnss << "-supertwist" << sskgrid[0] << sskgrid[1] << sskgrid[2];
+  fnss << "-supershift" << sskshift[0] << sskshift[1] << sskshift[2];
+  fnss << "-nscf.in";
+  stringstream p2xss;
+  p2xss << nscfFname;
+  p2xss << "-supertwist" << sskgrid[0] << sskgrid[1] << sskgrid[2];
+  p2xss << "-supershift" << sskshift[0] << sskshift[1] << sskshift[2];
+  p2xss << "-pw2x.in";
+
+  //cout << "nscf filename: " << fnss.str() << endl;
+  //cout << "pw2x filename: " << p2xss.str() << endl;
+
+  // Now write the files themselves
+  ofstream nscffile(fnss.str().c_str());
+  nscffile << nscfstring;
+  nscffile.close();
+
+  ofstream pw2xfile(p2xss.str().c_str());
+  pw2xfile << p2xstringss.str();
+  pw2xfile.close();
+
+
+}
+
+#endif