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* *
* Aflow STEFANO CURTAROLO - Duke University 2003-2019 *
* High-Throughput ab-initio Materials Discovery *
* *
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LATEST VERSION OF THE FILE: materials.duke.edu/AFLOW/README_AFLOW_AGL.TXT
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Thermal properties calculated using a quasi-harmonic Debye model.
This implementation in AFLOW written by Cormac Toher and Stefano Curtarolo,
and is described in the papers Phys. Rev. B 90, 90, 174107 (2014) and
Phys. Rev. Materials 1, 015401 (2017).
Based on the GIBBS program, described in the publications
Computer Physics Communications 158, 57-72 (2004) and
Journal of Molecular Structure (Theochem) 368, 245-255 (1996).
Please cite the 4 papers mentioned above in addition to the standard AFLOW
papers if you use results obtained using the AFLOW AGL code.
The Hugoniot calculation described in point (18) below was implemented
by Patrick Avery at University of Buffalo (email: psavery@buffalo.edu).
The current version of AGL can calculate the thermal conductivity, Debye temperature,
Gruneisen parameter, heat capacity, vibrational free energy, and other thermal properties,
as a function of temperature and pressure. The results are written in a variety of formats
in different output files. The main output file is named aflow.agl.out, and contains the
AGL results for the thermal conductivity at 300K, the traditional and acoustic Debye
temperatures, the Gruneisen parameter, the heat capacities at constant volume (Cv) and
constant pressure (Cp) at 300K, the thermal expansion at 300K, and the static and
isothermal bulk modulus at 300K. It also contains the results for the thermal conductivity,
Debye temperature, Gruneisen parameter, heat capacity, thermal expansion and bulk modulus
as function of temperature; and the Gibbs free energy, vibrational Helmholtz free energy,
vibrational internal energy, and vibrational entropy as a function of temperature. More
information can be found in the other main ouput file AGL.out, which contains the results
for the thermal properties and bulk moduli for all temperatures and pressures. The values
for the vibrational internal energy, vibrational free energy, entropy, heat capacity,
Debye temperature and Gruneisen parameter as a function of temperature at zero pressure
are written to the file AGL_THERMO, in a similar format to that used by the THERMO file
written by AFLOW APL. For further details on the output files written, see points (16)
and (17) below. Other results can be written and plotted by setting the appropriate
values in the aflow.in file, as described in point (17) below.
Results are also written in JSON format in two files: AGL_energy.json and
AGL_energy_structures.json. The file AGL_energy.json contains the results for
the DFT energy as a function of volume, the enthalpy as a function of pressure,
and the Gibbs free energy as a function of pressure and temperature. The file
AGL_energy_structures.json contains the energies, stresses and pressures for each
calculated structure, as well as the structures themselves and the distortions applied
to them.
AFLOW AGL expects a well relaxed structure on input. There is no additional relaxation
inside the AFLOW AGL. So, you have to prepare such a structure by a separate AFLOW run
using a relaxation mode for energy and/or forces.
When AFLOW AGL is run, it will first check for the existence of the required DFT
calculations. If these exist, then it will extract the required information and
proceed to calculate the thermal properties. If these do not exist, then it will
create the required directories and aflow.in files, and then stop. By running AFLOW
with the "--D" and "--multi" flags, AFLOW will then automatically descend into these
subdirectories and run the required electronic structure calculations, after which
it will stop. The user will then have to rename or delete the LOCK file in the main
directory, and the run AFLOW again to calculate the thermal properties. This
can all be performed within a submission script as in the following example:
aflow --multi -D $pathname/ >> log.$PBS_JOBID
mv $pathname/LOCK $pathname/LOCK.old
aflow --multi -D $pathname/ >> log.$PBS_JOBID
This procedure is similar to that required to run AFLOW APL.
1) To perform a AFLOW AGL calculation the following line has to be present in aflow.in:
[AFLOW_AGL]CALC
AFLOW checks for the existence of this line in aflow.in. If it does not exist,
then the job is not an AFLOW AGL calculation and no other AGL settings are read.
AGL can also be run from within other parts of AFLOW, such as from APL, in order to
obtain properties such as bulk modulus and equilibrium volume as a function of
temperature to be used within these other parts of AFLOW. In this case, AGL will run
and the other AGL settings in the aflow.in file will be read, even if the
"[AFLOW_AGL]CALC" line is not present.
2) The AFLOW AGL method requires a set of energy vs. volume data, which are obtained
from DFT calculations of a set of strained structures. The user has the possibility
to set the number of strained structures and the size of the strain step. These
parameters can be set by including the following lines in the aflow.in file:
[AFLOW_AGL]NSTRUCTURES=number
[AFLOW_AGL]STRAIN_STEP=number
The default setting is 28 structures and a step size of 0.01. The strain step size
corresponds to the value by which each lattice vector is shortened or lengthened for
each new strained structure.
3) The AFLOW AGL method allows the user to select what type of AFLOW DFT runs are performed
for each strained structure (see Calderon et al., Comp. Mat. Sci. 108A, 233-238 (2015)
for a description of the parameters used for the different calculation types). The
default option is to perform an AFLOW STATIC calculation for each strained structure,
which can be set by including the following lines in the aflow.in file:
[AFLOW_AGL]STATIC=ON
The other option is to run a RELAX_STATIC=2 calculation, which can be set by including
the following lines in the aflow.in file:
[AFLOW_AGL]RELAX_STATIC=ON
4) The AFLOW AGL method allows the user to select which form of the equation of state is
used to fit the (E, V) data. The options include numerical, Vinet (J. Phys. Condens.
Matter 1, 1941 (1989)), Birch-Murnaghan and spinodal (Baonza, Caceres, and Nunez,
Phys. Rev. B 51, 28 (1995)). These options can be selected by including the following
line in the aflow.in file :
[AFLOW_AGL]IEOS=number
The options are as follows:
IEOS=0: Numerical equation of state (default setting)
IEOS=1: Vinet equation of state
IEOS=2: Birch-Murnaghan equation of state
IEOS=3: Vinet equation fitting, but numerical calculation to obtain thermal properties
IEOS=4: Birch-Murnaghan equation fitting, but numerical calculation to obtain thermal
properties
IEOS=5: Spinodal (BCNT) equation of state
IEOS=6: Spinodal (BCNT) equation fitting, but numerical calculation to obtain thermal
properties
IEOS=-1: Number equation of state with minimal output, no plots generated or files
other than [system name].out are written
For the spinodal equation of state, the user also has the option to optimize the
non-linear parameter beta using the following:
[AFLOW_AGL]IOPT_G=number
The options are as follows:
IOPT_G=0: Beta is fixed to 0.85
IOPT_G=1: Beta is always optimized
IOPT_G=2: Beta is only optimized in the static calculation, and then this value is used
for the finite temperature calculations
5) The AFLOW AGL method allows the user to select whether or not to calculate the Debye
temperature self-consistently. These options can be selected by including the following
line in the aflow.in file:
[AFLOW_AGL]IDEBYE=number
The options are as follows:
IDEBYE=0: No self-consistent calculation of Debye temperature, Debye temperature calculated
from static bulk moduli (default)
IDEBYE=1: User contributed Debye temperatures
IDEBYE=2: Self-consistent calculation of Debye temperatures from adiabatic bulk moduli
IDEBYE=3: Debye temperature calculated from static bulk modulus at static equilibrium volume
IDEBYE=-1: Static calculation only, no finite temperature properties calculated
User contributed Debye temperatures should be given in the following format:
[AFLOW_AGL]DEBYE_TEMP_number=number
The first number is an integer corresponding to the number of the structure, while the second
number is the user's value of the Debye temperature for this structure.
6) The AFLOW AGL method allows the user to choose the details of how the (E, V) curve is fitted by
a polynomial, and in particularly how convex points in the (E, V) data are accounted for. This
allows the user to relax the concavity restrictions on the (E, V) data being used. These options
can be selected by including the following line in the aflow.in file:
[AFLOW_AGL]FIT_TYPE=number
The options are as follows:
FIT_TYPE=0: Fits only the first concave section of the (E, V) data. If this does not include the
minimum, it also includes a second concave section starting from the minimum, if such
a section exists. This is the default setting.
FIT_TYPE=1: Fits only (E, V) data points where the energy is monotonically decreasing until the
minimum energy is reached, and points where the energy is monotonically increasing
after the minimum energy is reached.
FIT_TYPE=2: Fits all (E, V) data points.
FIT_TYPE=3: Selects points using same method as for FIT_TYPE=1, but then fits these points by a
polynomial which is used to generate a new set smoothly concave (E, V) data points.
FIT_TYPE=4: Fits all points by a polynomial which is used to generate a new set of smoothly
concave (E, V) data points.
FIT_TYPE=5: The (E, V) data is read in from user-created file instead of being directly extracted
from the results of the electronic structure calculations.
Note that these fitting options should be used carefully, as they could give misleading results.
They are mainly useful for testing and debugging, and for in depth exploration of certain properties
of specific systems. For high-throughput data generation, use only the default option of FIT_TYPE=0,
as this is the safest. Also, be sure to check for warnings about data points being excluded from the
calculation. If a lot of points are excluded, you may want to recheck the (E, V) from the original
electronic structure calculations, and if it is very noisy it would be advisable to rerun these
calculations with a denser k-point mesh.
7) The AFLOW AGL method allows the user to set the value of the Poisson ratio to be used by including
the following line in the aflow.in file:
[AFLOW_AGL]POISSON_RATIO=number
The default value is 0.25.
The AFLOW AGL method can also call the AFLOW AEL method to calculate the Poisson ratio from the
elastic constants by including the following line in the aflow.in file:
[AFLOW_AGL]AEL_POISSON_RATIO=ON
This option will run the AEL method in full, calculating the Poisson ratio, bulk and shear moduli,
and other elastic properties. Note that running this method in conjunction with AGL will require
an additional aflow run followed by moving the LOCK file to a different location. See the README
file for AEL for more details on this method.
8) The AFLOW AGL method allows the user to set the number of temperature and pressure points to be used
in the calculation, as well as the size of the increments between each temperature or pressure point.
These values can be set by including the following lines in the aflow.in file:
[AFLOW_AGL]NPRESSURE=number
[AFLOW_AGL]SPRESSURE=number
[AFLOW_AGL]NTEMP=number
[AFLOW_AGL]STEMP=number
NPRESSURE is the number of pressure points and SPRESSURE is the increment between pressure points.
NTEMP is the number of temperature points and STEMP is the increment between temperature points.
The current default values are as follows:
NPRESSURE=101
SPRESSURE=1.0
NTEMP=201
STEMP=10.0
9) The AFLOW AGL method allows the user to provide specific pressure values to be used in the
calculations. This option can be selected by including the following line in the aflow.in file:
[AFLOW_AGL]SET_PRESSURE_VALUE=ON
Setting this option results in the specific pressure values being read in from the aflow.in file.
The default value is SETPRESSUREVALUE=OFF so that no specific values are read in. User specified
pressure values should be provided using the following format:
[AFLOW_AGL]PRESSURE_number=number
Note that the first pressure value should always be equal to 0.0. If this is not the case,
AFLOW AGL will give a warning and insert a value of 0.0 as the first pressure value. Also,
negative pressure values will result in AFLOW AGL exiting with an error.
10) The AFLOW AGL method allows the user to set the maximum number of convergence iterations
for the Gauss-Legendre and self-consistent Debye functions. This limit prevents these
functions from getting stuck in an infinite loop. This value can be set by including the
following line in the aflow.in file:
[AFLOW_AGL]MAX_LOOPS=number
The default value is 250.
11) The AFLOW AGL method allows the user to set the value of the energy for an infinite volume.
The purpose of this is to set the zero of the energy scale.
This value can be set by including the following line in the aflow.in file:
[AFLOW_AGL]EINF=number
The default value is 0.0.
12) The AFLOW AGL method allows the user to choose whether or not to write out the input file for
the original, non-AFLOW version of GIBBS. This can be useful for debugging and testing.
This option can be selected by including the following line in the aflow.in file:
[AFLOW_AGL]WRITE_GIBBS_INPUT=option
The AGL input will be written for WRITE_GIBBS_INPUT=ON. The default value is WRITE_GIBBS_INPUT=OFF,
which does not write out the file.
13) The AFLOW AGL method allows the user to choose whether or not to check the concavity and
location of the energy minimum of the (E, V) data calculated with VASP before starting the
GIBBS method. In order to fit the (E, V) data by a polynomial, the data points should be
concave and include a minimum. This option can be selected by including the following line
in the aflow.in file:
[AFLOWGIBBS]CHECK_EV_CONCAVITY=option
A value of CHECK_EV_CONCAVITY=ON causes the concavity check to be performed. The default value
is CHECK_EV_CONCAVITY=OFF so no concavity check is performed prior to the GIBBS method. The GIBBS
method will perform another concavity check after the (E, V) data has been passed to it, and
will return an error if the data is not concave.
Problems with the (E, V) data are usually the result of incompleteness of the electronic
structure calculation basis set or k-point grid. If CHECK_EV_CONCAVITY=ON and if the (E, V)
data is not concave, then AFLOW AGL doubles value of KPPRA to increase the number of k-points,
and creates a new set of directories containing aflow.in files with this new value of KPPRA.
The electronuc structure calculations are rerun with the increased number of k-points, and
the new set of (E, V) data is once again checked for concavity. This process is repeated until
a concave data set is obtained or the maximum number of concavity check iterations is reached.
The number of concavity check iterations can be set by including the following line in the
aflow.in file:
[AFLOW_AGL]MAX_CC_ITER=number
The default value for the maximum number of concavity check iterations is 1.
The AFLOW AGL method allows the user to choose whether or not to check that the (E, V) data
set includes the energy minimum. In order to get a good fit, the (E, V) data should contain
the minimum. This check can be initiated by including the following line in the aflow.in file:
[AFLOW_AGL]CHECK_EV_MIN=option
A value of CHECK_EV_MIN=ON causes the check of the location of the energy minimum to be performed.
The default value is CHECK_EV_MIN=OFF so no check is performed.
If CHECK_EV_MIN=ON, the (E, V) data is sorted in order of increasing volume. If the lowest energy
in the data set corresponds to the smallest or largest volume, then the (E, V) data set does
not include the minimum. Additional strained structures are then created until the (E, V) data
includes a minimum or the maximum number of minimum check iterations is reached. The number of
minimum check iterations can be set by including the following line in the aflow.in file:
[AFLOW_AGL]MAX_CM_ITER=number
The default value for the maximum number of minimum position check iterations is 5.
14) Since multiple different volume calculations are performed for a given system, there is a
certain amount of redundancy towards the failure of some of these calculations, and therefore
options have been implemented within AGL to allow for the skipping of one or more failed run.
Failed runs can be detected automatically (by the absence of the appropriate LOCK or OUTCAR
file in the directory), and the option of whether or not to skip these runs can be set by
including the following line in the aflow.in file:
[AFLOW_AGL]AUTOSKIP_FAILED_ARUNS=option
The default is "OFF" so that no runs are skipped automatically; instead detection of a failed
run will cause AGL to exit with an error unless this particular run was explicitly listed to
be skipped.
Specific runs can be listed for skipping by including the following line in the aflow.in file:
[AFLOW_AGL]SKIP_FAILED_ARUNS=directory_name_list
where "directory_name_list" is a string with the list of directory names containing the failed
runs to be skipped by the AGL fitting algorithm. If there is more than one failed run, the
individual directory names should be listed on the same line, separated by commas.
AGL only permits a certain number of runs to be skipped. The maximum number of runs permitted
to be skipped can be set by including the following line in the aflow.in file:
[AFLOW_AGL]SKIP_ARUNS_MAX=number
The default value is 7, so that up to seven runs can be skipped.
15) The AFLOW AGL method will automatically calculate the thermal conductivity at the acoustic
Debye temperature and as a function of temperature using the equation originally derived by
Slack (see Glen A. Slack, Solid State Physics 34, 1-75 (1979) for original method and
C. Toher et al., Phys. Rev. B 90, 174107 (2014) and Phys. Rev. Materials 1, 015401 (2017)
for more details; these references also describe the acoustic Debye temperature). This
calculation is always switched on.
The thermal conductivity can also be calculated with this equation as a function of
temperature using the equilibrium volume as a function of temperature by including
the following line in the aflow.in file:
[AFLOW_AGL]KAPPA_VOLUME=option
The thermal conductivity will be calculated using the equilibrium volume as a function
of temperature for KAPPA_VOLUME=ON, and the results are written to the file
"AGL_thermal_properties_temperature_vol.dat". The default value is KAPPA_VOLUME=OFF,
which only calculates the thermal conductivity using the equilibrium volume at the
acoustic Debye temperature.
The user can also provide values to AGL for the acoustic Debye temperature and the
Gruneisen parameter to be used in calculating the thermal conductivity by including
the lines:
[AFLOW_AGL]THETA_COND=number
[AFLOW_AGL]GRUNEISEN=number
If both of these lines are present, the thermal conductivity is calculated with the
Slack equation using the values provided by the user, and the results are written in
the "AGL_thermal_conductivity_user_lib.dat". This can be useful for comparing AGL
results to values in the literature for the purpose of debugging and testing the
AGL code.
16) The main output file for AFLOW AGL is aflow.agl.out. It contains the AGL results
for the thermal conductivity at 300K, the traditional and acoustic Debye temperatures,
the Gruneisen parameter, the heat capacities at constant volume (Cv) and constant
pressure (Cp) at 300K, the thermal expansion at 300K, and the static and isothermal
bulk modulus at 300K, as well as recording the source and value of the Poisson ratio
used to calculate the Debye temperature. It also contains the results for the thermal
conductivity, Debye temperature, Gruneisen parameter, heat capacity, thermal expansion
and bulk modulus as function of temperature; and the Gibbs free energy, vibrational
Helmholtz free energy, vibrational internal energy, and vibrational entropy as a
function of temperature.
17) The AFLOW AGL method allows the user to choose whether or not to automatically create
plots of the results for the Debye temperature, heat capacity, Gruneisen parameter, and
vibrational free energy as a function of temperature; as well as the energies obtained
from the DFT calculations as a function of volume per atom and volume per cell. These
plots are in saved as different formats depending on the input given by the user. The
plots are stored in the files _debye_temperature.*, _heat_capacity.*,
_gruneisen_parameter.*, _vibrational_free_energy.*,
__energy_volume_atom.* and __energy_volume_cell.*;
where "*" is dependent on the format in which the files are saved and is
the name given to the material system being calculated. These results can be plotted
by including the following line in the aflow.in file:
[AFLOW_AGL]PLOT_RESULTS=option
If PLOT_RESULTS=ON, then the plots are generated with gnuplot. The default option is
PLOT_RESULTS=OFF so that no plots are generated. Which files are kept and which formats
are used to save the plots depends on the options used to run AFLOW. In particular,
the "--keep" option controls whether or not the gnuplot script ("--keep=gnuplot")
and the eps file ("--keep=eps") are saved instead of deleted. The plots can be saved
in other file formats including png, pdf, jpeg and gif using the options "--keep=png",
"--keep=pdf", "--keep=jpg" and "--keep=gif", respectively.
If [AFLOW_AGL]IEOS=-1 or [AFLOW_AGL]IDEBYE=-1, then the plotting of these properties
is skipped.
The AFLOW AGL method also allows the user to choose whether to write additional output
files. These additional output files include the file Debye_temperature.dat, which
writes the Debye temperature, heat capacity, vibrational free energy and Gruneisen
parameter as a function of temperature in a format which is easy to plot using commonly
available graphing software such as xmgrace. This file can be written by including the
following entry in the aflow.in file:
[AFLOW_AGL]WRITE_FULL_RESULTS=option
The additional output files are written if WRITE_FULL_RESULTS=ON. The default value is
WRITE_FULL_RESULTS=OFF, i.e. the additional output files are not written. When this option
is active, the values of the Debye temperature, heat capacity, vibrational free energy
and Gruneisen parameter at certain temperatures are written in the file Debye_summary.dat.
These temperature values correspond to methods most often used in the literature to
determine which temperature value is used for the Debye temperature or heat capacity being
reported. If [AFLOW_AGL]IEOS=-1 or [AFLOW_AGL]IDEBYE=-1, then the writing of these files
is skipped. The specific temperature values are determined as follows:
- Best fit of Debye temperature to heat capacity:
The first temperature value is determined from the value of the Debye temperature which
produces the best fit to the heat capacity curve calculated using AGL. The heat capacity
curve is fitted using the following equation:
c_V = 9 n k_B (\\frac{T}{Theta_D})^3 \\int_0^{Theta_D / T} \\frac{x^4 e^x}{(e^x - 1)^2} dx
Here, c_V is the heat capacity at constant volume, n is the number of atoms in the unit
cell, k_B is Boltzmann's constant, T is the temperature, and Theta_D is the Debye temperature.
This equation is the same as that given in equation 23.26 in Solid State Physics, Ashcroft and
Mermin (1976). The temperature value at which this value of the Debye temperature is produced
by AGL is also written, along with the heat capacity, vibrational free energy, and
Gruneisen parameter at this temperature.
- Temperature where heat capacity is half Dulong-Petit value
At high temperatures, the heat capacity tends to a limit given by 3 n k_B, where n is the
number of atoms per unit cell and k_B is the Debye temperature. This is known as the
Dulong-Petit value. The second temperature value is determined from the point at which the
heat capacity is equal to half of this value, i.e. 1.5 n k_B. This method was used to determine
the Debye temperatures listed in table 23.3 in Solid State Physics, Ashcroft and Mermin (1976).
- Minimum value of Debye temperature
The third temperature value used it that at which the Debye temperature calculated
using the AGL method is a minimum.
- Maximum value of Debye temperature
The fourth temperature value used it that at which the Debye temperature calculated
using the AGL method is a maximum.
- 300K (~room temperature)
The final temperature used is 300K, which corresponds approximately to room temperature.
Finally, the values of the Debye temperature, Gruneisen parameter and vibrational free
energy for the temperatures corresponding to the best fit to the heat capacity, the half
Dulong-Petit value of the heat capacity, and 300K (~room temperature), respectively, are
written in a script-parsable format in the file agllib.dat. The format used is
the same as that used for the file aflowlib_entry.out.
18) The energy and mass density data as a function of temperature and pressure generated
by AGL can be used calculate the Hugoniot relation for the material. It finds the energy (E)
and mass density (rho) at each pressure (P) and temperature so that the following Hugoniot
expression is true:
E - E0 = 0.5 * (P + P0)*(1.0/rho0 - 1.0/rho)
where E0, P0 and rho0 are the reference energy, pressure and mass density for the material
(typically the values at room temperature and pressure). The Hugoniot relation can be
calculated using AGL by including the following line in the aflow.in file:
[AFLOW_AGL]HUGONIOT_CALC=option
If HUGONIOT_CALC=ON, then the Hugoniot calculation is performed and the results are written
to the file AGL_Hugoniot.out. The default option is HUGONIOT_CALC=ON so that the Hugoniot
calculation is performed automatically; this can be switched off by setting HUGONIOT_CALC=OFF.
If the solution of the Hugoniot relation is outside the range of calculated range, then an
extrapolation can be performed by including the following line in the aflow.in file:
[AFLOW_AGL]HUGONIOT_EXTRAPOLATE=option
If HUGONIOT_EXTRAPOLATE=ON, then the Hugoniot extrapolation is performed. The default option is
HUGONIOT_EXTRAPOLATE=OFF so that the Hugoniot extrapolation is not performed.
19) By default, if AGL cannot find a minimum of the energy at a particular temperature and pressure,
then it will truncate the pressure range so that it only runs up to that point. If this happens
at zero pressure, then the temperature range will also be truncated. This can be problematic
when trying to explore the high pressure/high temperature regime. Instead, the option to skip
over these points rather than truncate the pressure and temperature ranges can be selected by
including the following line in the aflow.in file:
[AFLOW_AEL]RUN_ALL_PRESSURE_TEMPERATURE=option
If this option is set to "ON", then it will skip over the pressure and temperature points where
it cannot find a minimum energy, saving the values of the thermodynamic quantities in a C++ struct.
When this option is set to "ON", many of the usual output files are not written, since many of the
usual quantities are not saved in the usual format, due to the skipping of pressure and temperature
points. The output files that are written are the AGL_energy.json file and AGL_energy_structures.json
files, where the thermodynamic properties for each pressure and temperature are stored in individual
JSON objects along with the corresponding temperature and pressure values.
If the option HUGONIOT_CALC=ON is selected but RUN_ALL_PRESSURE_TEMPERATURE=OFF, then AGL will automatically
check if the pressure or temperature ranges were truncated during the GIBBS algorithm. If they have been
truncated, then AGL will re-run the GIBBS algorithm with RUN_ALL_PRESSURE_TEMPERATURE=ON, so that the entire
requested pressure and temperature range is explored. Note that since all of the output files except for
the AGL_energy.json and AGL_Hugoniot.out files have already been written at this point, this does not
affect the writing of the other output files, and thus will result in the writing of all of the output
files that would normally be written.
20) Electronic properties as a function of pressure are automatically extracted from the electronic density
of states in the VASP DOSCAR files. The band gap (in the case of insulators and semiconductors) and
the value of the DOS at the Fermi energy (in the case of metals) as a function of pressure are calculated
and written in the files AGL_edos_gap_pressure.out and AGL_edos_gap_pressure.json. The band gap and
the DOS at the Fermi energy as a function of pressure are fitted by polynomials, and the evaluated values
at each pressure are also written to these files. The polynomials are used to calculated the derivative
with respect to pressure of the band gap and DOS at zero pressure, which is used to quantify the
sensitivity of the electronic structure to applied strains and pressure. These derivatives, along with
the minimum and maximum values of the DOS and band gap, are also written in the files
AGL_edos_gap_pressure.out and AGL_edos_gap_pressure.json.
21) EXAMPLE: CaO FCC with default AGL settings (note that this will give the same results if
all of the "[AFLOW_AGL]" lines except "[AFLOW_AGL]CALC" are removed or commented out):
[AFLOW] **************************************************************************************************************************
[AFLOW] Test file for AGL calculation of CaO (fcc)
[AFLOW] **************************************************************************************************************************
[AFLOW] **************************************************************************************************************************
[AFLOW]SYSTEM=Ca1O1_ICSD_26959
[AFLOW] **************************************************************************************************************************
[AFLOW] input file for aflow
[AFLOW_MODE=VASP]
[AFLOW] **************************************************************************************************************************
[AFLOW_MODE_ZIP=xz]
[AFLOW_MODE_BINARY=vasp46s]
[AFLOW] **************************************************************************************************************************
[AFLOW] **************************************************************************************************************************
[AFLOW_MODE_MPI]
[AFLOW_MODE_MPI_MODE]NCPUS=MAX
[AFLOW_MODE_MPI_MODE]COMMAND ="mpirun -np"
[AFLOW_MODE_MPI_MODE]AUTOTUNE
[AFLOW_MODE_MPI_MODE]BINARY="mpivasp46s"
[AFLOW] **************************************************************************************************************************
[AFLOW_SYMMETRY]CALC
#[AFLOW_SYMMETRY]SGROUP_WRITE
#[AFLOW_SYMMETRY]SGROUP_RADIUS=7.77
[AFLOW] **************************************************************************************************************************
#[AFLOW_NEIGHBOURS]CALC
[AFLOW_NEIGHBOURS]RADIUS=7.7
[AFLOW_NEIGHBOURS]DRADIUS=0.1
[AFLOW] **************************************************************************************************************************
#[AFLOW_APL]CALC // README_AFLOW_APL.TXT
[AFLOW_APL]ENGINE=DM // README_AFLOW_APL.TXT
[AFLOW_APL]DISMAG=0.015 // README_AFLOW_APL.TXT
[AFLOW_APL]MINATOMS=100 // README_AFLOW_APL.TXT
#[AFLOW_APL]SUPERCELL=3x3x3 // README_AFLOW_APL.TXT
[AFLOW_APL]DC=y // README_AFLOW_APL.TXT
[AFLOW_APL]DPM=y // README_AFLOW_APL.TXT
[AFLOW_APL]ZEROSTATE=y // README_AFLOW_APL.TXT
[AFLOW_APL]DOS=y // README_AFLOW_APL.TXT
[AFLOW_APL]TP=y // README_AFLOW_APL.TXT
[AFLOW_APL]TPT=0:2000:10 // README_AFLOW_APL.TXT
[AFLOW] **************************************************************************************************************************
#[AFLOW_QHA]CALC // README_AFLOW_QHA_SCQHA_QHA3P.TXT
[AFLOW_QHA]MODE=QHA3P // README_AFLOW_QHA_SCQHA_QHA3P.TXT
[AFLOW_QHA]EOS=y // README_AFLOW_QHA_SCQHA_QHA3P.TXT
[AFLOW] **************************************************************************************************************************
#[AFLOW_AAPL]CALC // README_AFLOW_APL.TXT
[AFLOW_AAPL]TDMAG=0.015 // README_AFLOW_APL.TXT
[AFLOW_AAPL]CUT_SHELL=4 // README_AFLOW_APL.TXT
[AFLOW_AAPL]CUT_RAD=4.5 // README_AFLOW_APL.TXT
[AFLOW_AAPL]SUMRULE=1E-5 // README_AFLOW_APL.TXT
[AFLOW_AAPL]BTE=FULL // README_AFLOW_APL.TXT
[AFLOW_AAPL]THERMALGRID=21x21x21 // README_AFLOW_APL.TXT
[AFLOW_AAPL]ISOTOPE=y // README_AFLOW_APL.TXT
[AFLOW_AAPL]CUMULATIVEK=y // README_AFLOW_APL.TXT
[AFLOW_AAPL]BOUNDARY=n // README_AFLOW_APL.TXT
[AFLOW_AAPL]NANO_SIZE=100 // README_AFLOW_APL.TXT
[AFLOW_AAPL]TCT=200:700:20 // README_AFLOW_APL.TXT
[AFLOW] **************************************************************************************************************************
#[VASP_RUN]RELAX_STATIC_BANDS=2 // GENERATE | STATIC | RELAX=N | RELAX_STATIC=N | STATIC_BANDS | RELAX_STATIC_BANDS=N | REPEAT_BANDS [,DS[,DD[,DSCF]]]
#[VASP_FORCE_OPTION]NEGLECT_NOMIX
[VASP_FORCE_OPTION]CHGCAR=OFF // ON | OFF (default ON)
#[VASP_FORCE_OPTION]KPOINTS=keyword[,keyword] // EVEN | ODD | KSHIFT_GAMMA_EVEN | KSHIFT_GAMMA_ODD | KSCHEME_MONKHORST_PACK | KSCHEME_GAMMA | GAMMA | KEEPK | IBZKPT
[VASP_FORCE_OPTION]SYM=ON // ON | OFF (default ON)
[VASP_FORCE_OPTION]AUTO_PSEUDOPOTENTIALS=potpaw_PBE // pot_LDA | pot_GGA | potpaw_LDA | potpaw_GGA | potpaw_PBE | potpaw_LDA_KIN | potpaw_PBE_KIN
[VASP_FORCE_OPTION]NBANDS // Estimate Bands (better than VASP)
#[VASP_FORCE_OPTION]SPIN=ON,REMOVE_RELAX_1 // (ON | OFF (default ON)), REMOVE_RELAX_1 | _2
#[VASP_FORCE_OPTION]AUTO_MAGMOM=ON // ON | OFF (default OFF)
[VASP_FORCE_OPTION]RELAX_MODE=ENERGY // ENERGY | FORCES | ENERGY_FORCES | FORCES_ENERGY (default ENERGY)
[VASP_FORCE_OPTION]PREC=HIGH // (LOW | MEDIUM | NORMAL | HIGH | ACCURATE), PRESERVED (default=MEDIUM)
[VASP_FORCE_OPTION]ALGO=FAST // (NORMAL | VERYFAST | FAST | ALL | DAMPED), PRESERVED (default=NORMAL)
#[VASP_FORCE_OPTION]NOTUNE
[VASP_FORCE_OPTION]TYPE=DEFAULT // METAL | INSULATOR | SEMICONDUCTOR | DEFAULT (default DEFAULT)
[VASP_FORCE_OPTION]CONVERT_UNIT_CELL=SPRIM // SPRIM, SCONV, NIGGLI, MINK, INCELL, COMPACT, WS, CART, FRAC, PRES
#[VASP_FORCE_OPTION]VOLUME+=10.0
#[VASP_FORCE_OPTION]VOLUME*=1.05
[AFLOW] **************************************************************************************************************************
[AFLOW] **************************************************************************************************************************
[VASP_INCAR_MODE_EXPLICIT]START
SYSTEM=Ca1O1_ICSD_26959
NELM = 120
NELMIN=2
LPLANE=.TRUE.
LREAL=.FALSE.
LSCALU=.FALSE.
#NBANDS=XX # for hand modification
#IALGO=48 # for hand modification
[VASP_INCAR_MODE_EXPLICIT]STOP
[AFLOW] **************************************************************************************************************************
[VASP_KPOINTS_MODE_IMPLICIT]
[VASP_KPOINTS_FILE]KSCHEME=M
[VASP_KPOINTS_FILE]KPPRA=8000
[VASP_KPOINTS_FILE]STATIC_KSCHEME=M
[VASP_KPOINTS_FILE]STATIC_KPPRA=10000
[VASP_KPOINTS_FILE]BANDS_LATTICE=FCC
[VASP_KPOINTS_FILE]BANDS_GRID=20
[AFLOW] **************************************************************************************************************************
[AFLOW_AGL]CALC
[AFLOW_AGL]AEL_POISSON_RATIO=OFF
[AFLOW_AGL]POISSON_RATIO=0.25
[AFLOW_AGL]NTEMP=201
[AFLOW_AGL]NPRESSURE=101
[AFLOW_AGL]NSTRUCTURES=28
[AFLOW_AGL]STRAIN_STEP=0.01
[AFLOW_AGL]WRITE_GIBBS_INPUT=OFF
[AFLOW_AGL]WRITE_FULL_RESULTS=OFF
[AFLOW_AGL]PLOT_RESULTS=OFF
[AFLOW_AGL]IEOS=0
[AFLOW_AGL]IDEBYE=0
[AFLOW_AGL]CHECK_EV_CONCAVITY=OFF
[AFLOW_AGL]CHECK_EV_MIN=OFF
[AFLOW_AGL]FIT_TYPE=0
[AFLOW_AGL]AUTOSKIP_FAILED_ARUNS=OFF
[AFLOW_AGL]SKIP_FAILED_ARUNS=
[AFLOW_AGL]SKIP_ARUNS_MAX=7
[AFLOW_AGL]HUGONIOT_CALC=ON
[AFLOW_AGL]RUN_ALL_PRESSURE_TEMPERATURE=OFF
[AFLOW] **************************************************************************************************************************
[VASP_POSCAR_MODE_EXPLICIT]START
Ca1O1 #225 - (Ca1O1_ICSD_26959) - Ca1O1 [Ca1O1] cF8 Fm-3m CaO 225 Ca1O1_ICSD_26959 ICSD_26959 (icsd library) (WICKOFF 225 #225) [FCC,FCC,cF8] (STD_PRIM doi:10.1016/j.commatsci.2010.05.010)
1.224745
0.00000000000000 1.95061033183634 1.95061033183634
1.95061033183634 0.00000000000000 1.95061033183634
1.95061033183634 1.95061033183634 0.00000000000000
1 1
Direct(2) [A1B1]
0.00000000000000 0.00000000000000 0.00000000000000 Ca
0.50000000000000 0.50000000000000 0.50000000000000 O
[VASP_POSCAR_MODE_EXPLICIT]STOP
[AFLOW] **************************************************************************************************************************
[VASP_POTCAR_MODE_IMPLICIT]
[VASP_POTCAR_FILE]Ca
[VASP_POTCAR_FILE]O
[AFLOW] potpaw_PBE: Ca_sv O
[AFLOW] COMPOSITION_PP=|Ca_sv1|O1|
[AFLOW] COMPOSITION=|Ca1|O1|
[AFLOW] VOLUME(A^3)=|0|0|
[AFLOW] MASS(amu)=|40.08|15.9994|
[AFLOW] **************************************************************************************************************************
[AFLOW] Aflow automatically generated (aflow_avasp.cpp)
[AFLOW] **************************************************************************************************************************
[AFLOW] aflow/aconvasp/aqe/apennsy v(30793) in ICSD/FCC/Ca1O1_ICSD_26959
[AFLOW] **************************************************************************************************************************
[AFLOW] SELF-MODIFICATION
[AFLOW] Recycling CONTCAR of relax1
[AFLOW] **************************************************************************************************************************
[VASP_POSCAR_MODE_EXPLICIT]START
Ca1O1 #225 - (Ca1O1_ICSD_26959) - Ca1O1
1.224745
0.00000000000000 1.97560216103176 1.97560216103176
1.97560216103176 0.00000000000000 1.97560216103176
1.97560216103176 1.97560216103176 -0.00000000000000
1 1
Direct(2) [A1B1]
0.00000000000000 -0.00000000000000 -0.00000000000000
0.50000000000000 0.50000000000000 0.50000000000000
[VASP_POSCAR_MODE_EXPLICIT]STOP
[AFLOW] **************************************************************************************************************************
[VASP_FORCE_OPTION]SPIN=OFF // Self Correction
[AFLOW] SELF-MODIFICATION
[AFLOW] Recycling CONTCAR of relax2
[AFLOW] **************************************************************************************************************************
[VASP_POSCAR_MODE_EXPLICIT]START
Ca1O1 #225 - (Ca1O1_ICSD_26959) - Ca1O1
1.224745
0.00000000000000 1.97560216103176 1.97560216103176
1.97560216103176 0.00000000000000 1.97560216103176
1.97560216103176 1.97560216103176 0.00000000000000
1 1
Direct(2) [A1B1]
0.00000000000000 0.00000000000000 0.00000000000000
0.50000000000000 0.50000000000000 0.50000000000000
[VASP_POSCAR_MODE_EXPLICIT]STOP
[AFLOW] **************************************************************************************************************************