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https://github.com/triqs/dft_tools
synced 2024-12-22 20:34:38 +01:00
implemented multiple ncsf VASP cycles
This commit is contained in:
Malte Schüler
parent
d61b55f0a4
commit
7a6450b6fa
@ -105,7 +105,7 @@ def dmft_cycle():
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ar['DMFT_input']['code_versions']["cthyb_version"] = cthyb_version.version
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ar['DMFT_input']['code_versions']["cthyb_git"] = cthyb_version.cthyb_hash
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ar['DMFT_input']['code_versions']["dft_tools_version"] = dft_tools_version.version
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ar['DMFT_input']['code_versions']["dft_tools_version"] = dft_tools_version.dft_tools_hash
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ar['DMFT_input']['code_versions']["dft_tools_git"] = dft_tools_version.dft_tools_hash
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if 'iteration_count' in ar['DMFT_results']:
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iteration_offset = ar['DMFT_results']['iteration_count']+1
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S.Sigma_iw = ar['DMFT_results']['Iterations']['Sigma_it'+str(iteration_offset-1)]
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@ -53,7 +53,7 @@ DMFT
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dmft script
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------------------------------
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Since the python script for performing the dmft loop pretty much resembles that presented in the tutorial on :ref:`srvo3`, we will not go into detail here but simply provide the script :ref:`nio.py`. Following Kunes et al. in `PRB 75 165115 (2007) <https://journals.aps.org/prb/abstract/10.1103/PhysRevB.75.165115>`_ we use :math:`U=8` and :math:`J=1`. We se;ect :math:`\beta=5` instead of :math:`\beta=10` to ease the problem slightly. For simplicity we fix the double-counting potential to :math:`\mu_{DC}=59` eV by::
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Since the python script for performing the dmft loop pretty much resembles that presented in the tutorial on :ref:`SrVO3 <srvo3>`, we will not go into detail here but simply provide the script :ref:`nio.py`. Following Kunes et al. in `PRB 75 165115 (2007) <https://journals.aps.org/prb/abstract/10.1103/PhysRevB.75.165115>`_ we use :math:`U=8` and :math:`J=1`. We se;ect :math:`\beta=5` instead of :math:`\beta=10` to ease the problem slightly. For simplicity we fix the double-counting potential to :math:`\mu_{DC}=59` eV by::
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DC_value = 59.0
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SK.calc_dc(dm, U_interact=U, J_hund=J, orb=0, use_dc_value=DC_value)
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@ -62,11 +62,11 @@ For sensible results run this script in parallel on at least 20 cores. As a quic
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Local lattice Green's function for all projected orbitals
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----------------------
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---------------------------------------------------------
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We calculate the local lattice Green's function - now also for the uncorrelated orbitals, i.e., the O p states, for what we use the script :ref:`NiO_local_lattice_GF.py`. The result is saved in the h5 file as `G_latt_orb_it<n_it>`, where `<n_it>` is the number of the last DMFT iteration.
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Spectral function on real axis: MaxEnt
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----------------------
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--------------------------------------
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To compare to results from literature we make use of the `maxent triqs application <https://triqs.github.io/maxent/master/>`_ and calculate the spectral function on real axis. Use this script to perform a crude but quick calculation: :ref:`maxent.py` using a linear real axis and a line-fit analyzer to determine the optimal :math:`\alpha`. The output is saved in the h5 file in `DMFT_results/Iterations/G_latt_orb_w_o<n_o>_it<n_it>`, where `<n_o>` is the number of the orbital and `n_it` is again the number of the last iteration. The real axis information is stored in `DMFT_results/Iterations/w_it<n_it>`.
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@ -74,26 +74,28 @@ To compare to results from literature we make use of the `maxent triqs applicati
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:width: 400
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:align: center
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.. Charge self-consistent DMFT
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.. ==================================================
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Charge self-consistent DMFT
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==================================================
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.. In this part we will perform charge self-consistent DMFT calculations. To do so we have to adapt the VASP `INCAR` such that :program:`VASP` reads the updated charge density after each step. We add the lines
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In this part we will perform charge self-consistent DMFT calculations. To do so we have to adapt the VASP `INCAR` such that :program:`VASP` reads the updated charge density after each step. We add the lines::
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.. ICHARG = 5
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.. NELM = 1000
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.. NELMIN = 1000
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ICHARG = 5
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NELM = 1000
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NELMIN = 1000
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.. which makes VASP wait after each step of its iterative diagonalization until the file vasp.lock is created. It then reads the update of the charge density in the file `GAMMA`. It is terminated by an external script after a desired amount of steps, such that we deactivate all automatic stoping criterion by setting the number of steps to a very high number.
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which makes VASP wait after each step of its iterative diagonalization until the file vasp.lock is created. It then reads the update of the charge density in the file `GAMMA`. It is terminated by an external script after a desired amount of steps, such that we deactivate all automatic stoping criterion by setting the number of steps to a very high number.
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.. We take the respective converged DFT and DMFT calculations from before as a starting point. I.e., we copy the `CHGCAR` and `nio.h5` together with the other :program:`VASP` input files and :file:`plo.cfg` in a new directory. We use a script called :program:`vasp_dmft` to invoke :program:`VASP` in the background and start the DMFT calculation together with :program:`plovasp` and the converter. This script assumes that the dmft sript contains a function `dmft_cycle()` and also the conversion from text files to the h5 file. Additionally we have to add a few lines to calculate the density correction and calculate the correlation energy. We adapt the script straightforardly and call it :ref:`nio_csc.py`. The most important new lines are
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We take the respective converged DFT and DMFT calculations from before as a starting point. I.e., we copy the `CHGCAR` and `nio.h5` together with the other :program:`VASP` input files and :file:`plo.cfg` in a new directory. We use a script called :program:`vasp_dmft` to invoke :program:`VASP` in the background and start the DMFT calculation together with :program:`plovasp` and the converter. This script assumes that the dmft sript contains a function `dmft_cycle()` and also the conversion from text files to the h5 file. Additionally we have to add a few lines to calculate the density correction and calculate the correlation energy. We adapt the script straightforardly (for a working example see :ref:`nio_csc.py`). The most important new lines are::
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.. SK.chemical_potential = SK.calc_mu( precision = 0.000001 )
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.. SK.calc_density_correction(dm_type='vasp')
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.. correnerg = 0.5 * (S.G_iw * S.Sigma_iw).total_density()
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SK.chemical_potential = SK.calc_mu( precision = 0.000001 )
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SK.calc_density_correction(dm_type='vasp')
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correnerg = 0.5 * (S.G_iw * S.Sigma_iw).total_density()
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.. where the chemical potential is determined to a greater precision than before, the correction to the dft density matrix is calculated and output to the file :file:`GAMMA`. The correlation energy is calculated via Migdal-Galitzki formula. We also slightly increase the tolerance for the detection of blocks since the DFT calculation now includes some QMC noise.
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where the chemical potential is determined to a greater precision than before, the correction to the dft density matrix is calculated and output to the file :file:`GAMMA`. The correlation energy is calculated via Migdal-Galitzki formula. We also slightly increase the tolerance for the detection of blocks since the DFT calculation now includes some QMC noise.
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.. We can start the whole machinery by excectuing
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To help convergence, we keep the density (i.e., the GAMMA file) fixed for a few DFT iterations. We do so since VASP uses an iterative diagonalization.
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.. vasp_dmft -n <n_procs> -i <n_iters> -p <vasp_exec> nio_csc.py
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We can start the whole machinery by excecuting::
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vasp_dmft -n <n_procs> -i <n_iters> -j <n_iters_dft> -p <vasp_exec> nio_csc.py
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@ -140,6 +140,7 @@ class ElectronicStructure:
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ions = sorted(list(set([param['isite'] for param in self.proj_params])))
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nions = len(ions)
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norb = nproj / nions
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print nproj, ns, nk, nb, ions, nions, norb
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# Spin factor
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sp_fac = 2.0 if ns == 1 and not self.nc_flag else 1.0
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@ -162,12 +163,15 @@ class ElectronicStructure:
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for ispin in xrange(ns):
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print
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print " Spin:", ispin + 1
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print self.proj_params
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for io, ion in enumerate(ions):
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print " Site:", ion
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iorb_inds = [(ip, param['m']) for ip, param in enumerate(self.proj_params) if param['isite'] == ion]
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print iorb_inds
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norb = len(iorb_inds)
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dm = np.zeros((norb, norb))
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ov = np.zeros((norb, norb))
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norb2 = self.proj_params[0]['l']*2+1
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dm = np.zeros((norb2, norb2))
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ov = np.zeros((norb2, norb2))
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for ind, iorb in iorb_inds:
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for ind2, iorb2 in iorb_inds:
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dm[iorb, iorb2] = den_mat[ispin, ind, ind2]
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@ -32,6 +32,7 @@ import signal
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import sys
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import pytriqs.utility.mpi as mpi
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import converter
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from shutil import copyfile
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xch = sys.excepthook
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def excepthook(typ, value, traceback):
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@ -40,7 +41,7 @@ def excepthook(typ, value, traceback):
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mpi.MPI.COMM_WORLD.Abort(1)
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sys.excepthook = excepthook
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debug = True
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debug = False
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#
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# Helper functions
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#
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@ -99,7 +100,7 @@ class bcolors:
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#
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# Main self-consistent cycle
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#
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def run_all(vasp_pid, dmft_cycle, cfg_file, n_iter):
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def run_all(vasp_pid, dmft_cycle, cfg_file, n_iter, n_iter_dft, vasp_version):
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"""
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"""
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mpi.report(" Waiting for VASP lock to appear...")
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@ -120,6 +121,7 @@ def run_all(vasp_pid, dmft_cycle, cfg_file, n_iter):
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mpi.report(" VASP stopped")
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vasp_running = False
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break
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# Tell VASP to stop if the maximum number of iterations is reached
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iter += 1
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if iter == n_iter:
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@ -154,10 +156,31 @@ def run_all(vasp_pid, dmft_cycle, cfg_file, n_iter):
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print " DFT DC: ", dft_dc
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print "="*80
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print
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if mpi.is_master_node() and vasp_running:
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open('./vasp.lock', 'a').close()
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# check if we should do additional VASP calculations
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# in the standard VASP version, VASP writes out GAMMA itself
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# so that if we want to keep GAMMA fixed we have to copy it to
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# GAMMA_recent and copy it back after VASP has completed an iteration
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# if we are using a hacked Version of VASP where the write out is
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# disabled we can skip this step.
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# the hack consists of removing the call of LPRJ_LDApU in VASP src file
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# electron.F around line 644
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iter_dft = 0
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if vasp_version == 'standard':
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copyfile(src='GAMMA',dst='GAMMA_recent')
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while iter_dft < n_iter_dft:
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if mpi.is_master_node():
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open('./vasp.lock', 'a').close()
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while is_vasp_lock_present():
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time.sleep(1)
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if not is_vasp_running(vasp_pid):
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mpi.report(" VASP stopped")
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vasp_running = False
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break
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iter_dft += 1
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if vasp_version == 'standard':
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copyfile(src='GAMMA_recent',dst='GAMMA')
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if mpi.is_master_node():
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total_energy = dft_energy + corr_energy - dft_dc
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with open('TOTENERGY', 'w') as f:
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@ -170,7 +193,9 @@ def run_all(vasp_pid, dmft_cycle, cfg_file, n_iter):
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mpi.report("***Done")
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def main():
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import importlib
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try:
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vasp_pid = int(sys.argv[1])
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except (ValueError, KeyError):
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@ -184,19 +209,34 @@ def main():
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if mpi.is_master_node():
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print "ERROR: Number of iterations must be provided as the second argument"
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raise
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try:
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n_iter_dft = int(sys.argv[3])
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except (ValueError, KeyError):
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if mpi.is_master_node():
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print "ERROR: Number of VASP iterations with fixed charge density must be provided as the third argument"
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raise
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try:
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dmft_script = re.sub("\.py$", "", sys.argv[3])
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dmft_script = re.sub("\.py$", "", sys.argv[4])
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except:
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if mpi.is_master_node():
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print "ERROR: User-defined DMFT script must be provided as the third argument"
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print "ERROR: User-defined DMFT script must be provided as the fourth argument"
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raise
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# Optional parameter: config-file name
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try:
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cfg_file = sys.argv[4]
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cfg_file = sys.argv[5]
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except KeyError:
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cfg_file = 'plo.cfg'
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try:
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vasp_version = sys.argv[6]
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except KeyError:
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vasp_version = 'standard'
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if vasp_version != 'standard' and vasp_version != 'no_gamma_write':
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raise Exception('vasp_version has to be standard or no_gamma_write')
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# if len(sys.argv) > 1:
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# vasp_path = sys.argv[1]
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@ -211,7 +251,7 @@ def main():
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dmft_mod = importlib.import_module(dmft_script)
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run_all(vasp_pid, dmft_mod.dmft_cycle, cfg_file, n_iter)
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run_all(vasp_pid, dmft_mod.dmft_cycle, cfg_file, n_iter, n_iter_dft, vasp_version)
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if __name__ == '__main__':
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main()
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@ -5,9 +5,9 @@ MPIRUN_CMD=mpirun
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show_help()
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{
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echo "
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Usage: vasp_dmft [-n <number of cores>] -i <number of iterations> [-p <path to VASP directory>] [<dmft_script.py>]
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Usage: vasp_dmft [-n <number of cores>] -i <number of iterations> -j <number of VASP iterations with fixed charge density> [-v <VASP version>] [-p <path to VASP directory>] [<dmft_script.py>]
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If the number of cores is note specified it is set to 1 by default.
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If the number of cores is not specified it is set to 1 by default.
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<dmft_script.py> must provide an importable function 'dmft_cycle()' which is invoked
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once per DFT+DMFT iteration. If the script name is omitted the default name
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@ -18,7 +18,7 @@ Usage: vasp_dmft [-n <number of cores>] -i <number of iterations> [-p <path to V
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"
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}
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while getopts ":n:i:p:" opt; do
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while getopts ":n:i:j:v:p:h" opt; do
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case $opt in
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n)
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# echo "Option: Ncpu, argument: $OPTARG"
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@ -34,11 +34,27 @@ while getopts ":n:i:p:" opt; do
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# echo "Number of iterations: $NITER"
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fi
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;;
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j)
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# echo "Option: Ndftiter"
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if [ -n "$OPTARG" ]; then
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NDFTITER=$OPTARG
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# echo "Number of iterations with fixed density: $NDFTITER"
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fi
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;;
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p)
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if [ -n "$OPTARG" ]; then
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VASP_DIR=$OPTARG
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fi
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;;
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v)
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if [ -n "$OPTARG" ]; then
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VASP_VERSION=$OPTARG
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fi
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;;
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h)
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show_help
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exit 1
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;;
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:)
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echo " Error: Option -$OPTARG requires an argument" >&2
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show_help
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@ -55,6 +71,7 @@ if [ -z "$NITER" ]; then
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exit 1
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fi
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if [ -z "$VASP_DIR" ]; then
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echo " Error: A path to VASP directory must be given either with option -p or by setting variable VASP_DIR" >&2
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show_help
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@ -66,6 +83,16 @@ if [ -z "$NPROC" ]; then
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NPROC=1
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fi
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if [ -z "$NDFTITER" ]; then
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echo " Number of VASP iterations without updating density not specified, setting to 1"
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NDFTITER=1
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fi
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if [ -z "$VASP_VERSION" ]; then
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echo " VASP version not specified, setting to standard"
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VASP_VERSION="standard"
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fi
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shift $((OPTIND-1))
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if [ -z "$1" ]; then
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@ -76,11 +103,14 @@ fi
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echo " Number of cores: $NPROC"
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echo " Number of iterations: $NITER"
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echo " Number of iterations with fixed density: $NDFTITER"
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echo " VASP version: $VASP_VERSION"
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echo " Script name: $DMFT_SCRIPT"
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rm -f vasp.lock
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stdbuf -o 0 $MPIRUN_CMD -np $NPROC "$VASP_DIR" &
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# stdbuf -o 0 $MPIRUN_CMD -np $NPROC "$VASP_DIR" &
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vasp_intel.sh &
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$MPIRUN_CMD -np $NPROC python -m triqs_dft_tools.converters.plovasp.sc_dmft $(jobs -p) $NITER $DMFT_SCRIPT 'plo.cfg' || kill %1
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$MPIRUN_CMD -np $NPROC python -m triqs_dft_tools.converters.plovasp.sc_dmft $(jobs -p) $NITER $NDFTITER $DMFT_SCRIPT 'plo.cfg' $VASP_VERSION || kill %1
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