new VASP 6.5.0 hdf5 support capability (#262)

* [vasp] read fermi from vasp h5 archive and write deltaN to vasp h5 archive
* Reading vasptriqs.h5 file; reading GAMMA file for non-collinear full csc
* fix read error for tetrahedron data and eigs properties
* write deltaN only to vasp h5 if present, write to GAMMA text file only for old interface
* support symmetries at DFT level in VASP
* use IBZ kpoint list for writing GAMMA vaspgamma.h5
* make vaspgamma.h5 default
* write n_k_ibz into dft_misc_input so in can be used inside of sumk
* add new svo converter test

---------

Co-authored-by: Dario Fiore Mosca <[email protected]>

python/triqs_dft_tools/converters/plovasp/elstruct.py

@@ -39,6 +39,7 @@ class ElectronicStructure:
 
     - *natom* (int) : total number of atoms
     - *nktot* (int) : total number of `k`-points
+    - *nkibz* (int) : number of `k`-points in IBZ
     - *nband* (int) : total number of bands
     - *nspin* (int) : spin-polarization
     - *nc_flag* (True/False) : non-collinearity flag
@@ -58,8 +59,9 @@ def __init__(self, vasp_data):
         self.natom = vasp_data.poscar.nq
         self.type_of_ion = vasp_data.poscar.type_of_ion
         self.nktot = vasp_data.kpoints.nktot
+        self.nkibz = vasp_data.kpoints.nkibz
 
-        self.kmesh = {'nktot': self.nktot}
+        self.kmesh = {'nktot': self.nktot, 'nkibz': self.nkibz}
         self.kmesh['kpoints'] = vasp_data.kpoints.kpts
         # VASP.6.
         self.nc_flag = vasp_data.plocar.nc_flag
@@ -86,21 +88,15 @@ def __init__(self, vasp_data):
 
 # Check that the number of k-points is the same in all files
         _, ns_plo, nk_plo, nb_plo = vasp_data.plocar.plo.shape
-        assert nk_plo == self.nktot, "PLOCAR is inconsistent with IBZKPT (number of k-points)"
+        assert nk_plo == self.nktot, "PLOCAR is inconsistent with IBZKPT (number of k-points). If you run VASP with symmetry make sure to use the h5 interface of the converter, i.e. have the locproj information written to vaspout.h5"
 
 # FIXME: Reading from EIGENVAL is obsolete and should be
 #        removed completely.
-#        if not vasp_data.eigenval.eigs is None:
-        if False:
+        if vasp_data.eigenval.eigs is not None:
             print("eigvals from EIGENVAL")
             self.eigvals = vasp_data.eigenval.eigs
             self.ferw = vasp_data.eigenval.ferw.transpose((2, 0, 1))
-
-            nk_eig = vasp_data.eigenval.nktot
-            assert nk_eig == self.nktot, "PLOCAR is inconsistent with EIGENVAL (number of k-points)"
-
-# Check that the number of band is the same in PROJCAR and EIGENVAL
-            assert nb_plo == self.nband, "PLOCAR is inconsistent with EIGENVAL (number of bands)"
+            self.efermi = vasp_data.doscar.efermi
         else:
             print("eigvals from LOCPROJ")
             self.eigvals = vasp_data.plocar.eigs
@@ -151,7 +147,7 @@ def debug_density_matrix(self):
 
 # Spin factor
         sp_fac = 2.0 if ns == 1 and self.nc_flag == False else 1.0
-        
+
         if self.nc_flag == False:
             den_mat = np.zeros((ns, nproj, nproj), dtype=float)
             overlap = np.zeros((ns, nproj, nproj), dtype=float)
@@ -184,9 +180,9 @@ def debug_density_matrix(self):
                         out += "    "
                         out += ''.join(map("{0:12.7f}".format, dov))
                         print(out)
-                    
-                    
-                    
+
+
+
         else:
             print("!! WARNING !! Non Collinear Routine")
             den_mat = np.zeros((ns, nproj, nproj), dtype=float)

python/triqs_dft_tools/converters/plovasp/plotools.py

@@ -289,6 +289,8 @@ def ctrl_output(conf_pars, el_struct, ng):
 
      * *nk*: number of `k`-points
 
+     * *nkibz*: number of `k`-points in IBZ
+
      * *ns*: number of spin channels
 
      * *nc_flag*: collinear/noncollinear case (False/True)
@@ -309,6 +311,7 @@ def ctrl_output(conf_pars, el_struct, ng):
 # Construct the header dictionary
     head_dict['ngroups'] = ng
     head_dict['nk'] = el_struct.kmesh['nktot']
+    head_dict['nkibz'] = el_struct.kmesh['nkibz']
     head_dict['ns'] = el_struct.nspin
     head_dict['kvec1'] = list(el_struct.structure['kpt_basis'][:,0])
     head_dict['kvec2'] = list(el_struct.structure['kpt_basis'][:,1])

python/triqs_dft_tools/converters/plovasp/sc_dmft.py

@@ -72,22 +72,26 @@ def is_vasp_running(vasp_pid):
     pid_exists = mpi.bcast(pid_exists)
     return pid_exists
 
+
 def get_dft_energy():
     """
-    Reads energy from the last line of OSZICAR.
+    Reads DFT energy from the last line of Vasp's OSZICAR or from vasptriqs.h5
     """
-    with open('OSZICAR', 'r') as f:
-        nextline = f.readline()
-        while nextline.strip():
-            line = nextline
-            nextline = f.readline()
-#            print "OSZICAR: ", line[:-1]
+    h5_energy = False
+    if os.path.isfile('vaspout.h5'):
+        with HDFArchive('vaspout.h5', 'r') as h5:
+            if 'oszicar' in h5['intermediate/ion_dynamics']:
+                dft_energy = h5['intermediate/ion_dynamics/oszicar'][-1,1]
+                h5_energy = True
 
-    try:
+    # as backup use OSZICAR file
+    if not h5_energy:
+        with open('OSZICAR', 'r') as file:
+            nextline = file.readline()
+            while nextline.strip():
+                line = nextline
+                nextline = file.readline()
         dft_energy = float(line.split()[2])
-    except ValueError:
-        print("Cannot read energy from OSZICAR, setting it to zero")
-        dft_energy = 0.0
 
     return dft_energy
 
@@ -98,9 +102,8 @@ class bcolors:
     YELLOW = '\033[93m'
     RED = '\033[91m'
     ENDC = '\033[0m'
-#
+
 # Main self-consistent cycle
-#
 def run_all(vasp_pid, dmft_cycle, cfg_file, n_iter, n_iter_dft, vasp_version):
     """
     """
@@ -117,15 +120,14 @@ def run_all(vasp_pid, dmft_cycle, cfg_file, n_iter, n_iter_dft, vasp_version):
         mpi.barrier()
         while is_vasp_lock_present():
             time.sleep(1)
-#            if debug: print bcolors.YELLOW + " waiting: rank %s"%(mpi.rank) + bcolors.ENDC
+            if debug: print(bcolors.YELLOW + " waiting: rank %s"%(mpi.rank) + bcolors.ENDC)
             if not is_vasp_running(vasp_pid):
                 mpi.report("  VASP stopped")
                 vasp_running = False
                 break
 
-# Tell VASP to stop if the maximum number of iterations is reached
-
-
+        # Tell VASP to stop if the maximum number of iterations is reached
+
         if debug: print(bcolors.MAGENTA + "rank %s"%(mpi.rank) + bcolors.ENDC)
         err = 0
         exc = None
@@ -161,7 +163,7 @@ def run_all(vasp_pid, dmft_cycle, cfg_file, n_iter, n_iter_dft, vasp_version):
         # electron.F around line 644
         iter_dft = 0
 
-        if vasp_version == 'standard':
+        if vasp_version == 'standard' or vasp_version == 'ncl':
             copyfile(src='GAMMA',dst='GAMMA_recent')
         while iter_dft < n_iter_dft:
             # insert recalculation of GAMMA here
@@ -190,7 +192,7 @@ def run_all(vasp_pid, dmft_cycle, cfg_file, n_iter, n_iter_dft, vasp_version):
                     vasp_running = False
                     break
             iter_dft += 1
-            if vasp_version == 'standard':
+            if vasp_version == 'standard' or vasp_version == 'ncl':
                 copyfile(src='GAMMA_recent',dst='GAMMA')
         iter += 1
         if iter == n_iter:
@@ -253,8 +255,8 @@ def main():
     except KeyError:
         vasp_version = 'standard'
 
-    if vasp_version != 'standard' and vasp_version != 'no_gamma_write':
-        raise Exception('vasp_version has to be standard or no_gamma_write')
+    #if vasp_version != 'standard' and vasp_version != 'no_gamma_write':
+    #    raise Exception('vasp_version has to be standard or no_gamma_write')
 
 #    if len(sys.argv) > 1:
 #        vasp_path = sys.argv[1]