# This is an example workflow going from

# specifying a crystal structure to

# constructing part of a phase diagram.
#
# It is assumed that CASM v1.2.0 is installed.
#

# in the ZrO example directory:

root=`pwd`

casm status -n

### Initialize project

casm init

### Set composition axes

casm status -n
casm composition --calc
casm composition --select 1

### Enumerate configurations

casm status -n
casm enum --method ScelEnum --max 4
casm enum --method ConfigEnumAllOccupations --all

### Enable VESTA visualization,

# Correct command depends on your system
# On Mac, often: 'casm.view "open -a /Applications/VESTA/VESTA.app"'
# On Linux: 'casm.view VESTA'
casm settings --set-view-command 'casm.view "open -a
/Applications/VESTA/VESTA.app"'
casm view SCEL4_2_2_1_0_0_0/12

### Calculate DFT energies

casm status -n
casm select --set-on

# set path to VASP pp by changing 'POTCAR_DIR_PATH' variable

emacs training_data/settings/calctype.default/SPECIES

# set VASP INCAR settings

emacs training_data/settings/calctype.default/INCAR

# set KPOINTS, either Auto, or

# to be scaled to match density determined from
# training_data/settings/calctype.default/POSCAR
emacs training_data/settings/calctype.default/KPOINTS

# set cluster submission parameters and convergence criteria

emacs training_data/settings/calctype.default/calc.json

# setup VASP jobs for manual checking

# (optional, skip if no VASP pseudopotentials)
casm calc --setup

# Can't actually submit jobs, would use:

# casm calc --submit
# casm update
# Instead, copy calculation results:
cp -r _casm_with_properties/jsonDB/* .casm/jsonDB/
casm status -d

### Set chemical reference

casm ref --set-auto
# Should output:
# Global chemical reference:
# Zr(1): -8.54698
# O(0.5)Zr(0.5): -9.0907

### Specify basis set

# Modify 'bspecs.json' as desired to specify orbits & basis functions

# (for this demo, don't actually change)
emacs basis_sets/bset.default/bspecs.json
casm bset -u

### Select configurations

casm select --set 'is_calculated' -o calculated.json

### Query properties

casm query -c CALCULATED -k 'corr formation_energy' -o fitting_data.json

### ECI fitting

# Create a directory for fitting work

cd $root/fit_1

# Create new eci setting

casm settings --new-eci test

# Select structures to fit with

casm select --set 'lt(comp(a),0.695)' -o all_lt_0p7
casm select -c all_lt_0p7 --set-off 'not(is_calculated)' -o train

# Create a 'casm-learn' input file

casm learn --exGeneticAlgorithm > fit_1_ga.json

# For demo purposes, a quicker calculation will suffice.

# Change "feature_selection"/"kwargs"/"evolve_params_kwargs"/"n_repetition": 5 or
10
emacs fit_1_ga.json

# Run 'casm-learn'
casm learn -s fit_1_ga.json

# Check results
casm learn -s fit_1_ga.json --hall
casm learn -s fit_1_ga.json --checkhull --indiv 0
python plot_hull.py

# Select ECI to use

casm learn -s fit_1_ga.json --select 0

### Run Monte Carlo

# semi-grand canonical setup

cd $root/mc/example_grand_canonical
casm format --monte

# edit metropolis_grand_canonical.json as desired

# run
casm monte -s metropolis_grand_canonical.json --verbosity verbose

# check results
cat results.json
cat results.csv

# very basic Python script showing how to plot MC data

python plot.py

### Using provided Monte Carlo results to construct a phase diagram

# For consistency, switch to 'default' ECI provided with demo

casm settings --set-eci default

# Low temperature expansion to get free energy reference states

# lte1 setup
cd $root/mc/example_lte1

# edit lte1_grand_canonical.json as desired

# run
casm monte -s lte1_grand_canonical.json

# check results
cat results.csv
cat results.json
python plot.py

# An example script for running a coarse grid of Monte Carlo calculations

cd $root/ZrO/mc/grid
python run.py

# Use pre-computed monte carlo fine grid results

cd $root/ZrO/mc/fine_grid
tar -xzvf results.tar.gz
python parse.py

# The 'plot_vary_T.py' and 'plot_vary_xi.py' scripts "animate" a range of

# Monte Carlo calculation paths by repeatedly plotting for a scan of parameters.
# To see the next plot, close the current one.

# check results for paths with varying T

python plot_vary_T.py
python plot_vary_T_all.py

# check results for paths with varying parameteric chemical potential

python plot_vary_xi.py
python plot_vary_xi_all.py

# free energy integration

python free_energy.py

# find phase boundary

python plot_phi_vary_xi.py
python plot_boundary_vary_xi.py