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| Original file line number | Diff line number | Diff line change |
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| """Interface with [elphmod](https://github.com/janberges/elphmod) MD driver.""" | ||
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| import sys | ||
| from .dummy import Dummy_driver | ||
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| __DRIVER_NAME__ = "elphmod" | ||
| __DRIVER_CLASS__ = "ModelIIIDriver" | ||
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| ERROR_MSG = """ | ||
| A pickled driver instance is required (see elphmod.md.Driver.save). | ||
| Example: python3 driver.py -u -m elphmod -o driver.pickle | ||
| """ | ||
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| class ModelIIIDriver(Dummy_driver): | ||
| """Wrapper around elphmod MD driver.""" | ||
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| def check_arguments(self): | ||
| """Check arguments and load driver instance.""" | ||
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| import elphmod | ||
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| if len(self.args) != 1: | ||
| sys.exit(ERROR_MSG) | ||
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| self.driver = elphmod.md.Driver.load(self.args[0]) | ||
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| def __call__(self, cell, pos): | ||
| """Calculate energy and forces for given structure.""" | ||
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| return self.driver(cell, pos) |
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| *.Wmat | ||
| *.epmatwp | ||
| *.ifc | ||
| *.pickle | ||
| *.wigner | ||
| *.xyz | ||
| *_hr.dat | ||
| RESTART | ||
| !driver.xyz |
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| # Makefile for the elphmod example | ||
| # | ||
| # This file is part of i-PI. | ||
| # i-PI Copyright (C) 2014-2024 i-PI developers | ||
| # See the "licenses" directory for full license information. | ||
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| .PHONY: all model driver run run2 plot clean | ||
| all: plot | ||
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| IPI = i-pi | ||
| MODEL = model_hr.dat model.ifc model.epmatwp model.wigner | ||
| DRIVER = driver.pickle driver.xyz | ||
| RUN = run.out run.pos_0.xyz run.for_0.xyz | ||
| PLOT = plot.pdf | ||
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| model $(MODEL): model.py | ||
| python3 $< | ||
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| driver $(DRIVER): driver.py $(MODEL) | ||
| python3 $< | ||
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| run $(RUN): input.xml $(DRIVER) | ||
| $(IPI) $< & | ||
| sleep 5 | ||
| i-pi-driver-py -u -m elphmod -o $(word 2,$^) | ||
| wait | ||
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| run2: input.xml run.py $(DRIVER) | ||
| $(IPI) $< & | ||
| sleep 5 | ||
| python3 $(word 2,$^) | ||
| wait | ||
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| plot $(PLOT): plot.py $(RUN) | ||
| python3 $< | ||
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| clean: | ||
| rm -rf $(MODEL) $(DRIVER) $(RUN) $(PLOT) RESTART EXIT '#'* |
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| elphmod - i-PI example | ||
| ====================== | ||
|
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| This example connects i-PI with [elphmod](https://github.com/janberges/elphmod), | ||
| which provides energy surfaces for distorted systems based on *ab initio* data | ||
| for the symmetric one, using the approximation of a linearized electron-lattice | ||
| coupling. This realizes *model III* by Schobert *et al.*, [SciPost Phys. **16**, | ||
| 046 (2024)](https://doi.org/10.21468/SciPostPhys.16.2.046). | ||
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| The Python packages `elphmod` and `matplotlib` (for plotting only) are required. | ||
| Both can be installed with `pip` or from `conda-forge`. | ||
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| This example performs the structural optimization of a charge-density wave in | ||
| monolayer tantalum disulfide. Running `make` performs the following steps: | ||
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| 1. Usually, the calculation is based on a Wannier Hamiltonian from Wannier90 | ||
| (`model_hr.dat`), force constants from the PHonon code of Quantum ESPRESSO | ||
| (`model.ifc`), and the corresponding representation of the coupling from a | ||
| [patched version](https://github.com/janberges/elphmod/tree/master/patches) | ||
| of the EPW code (`model.epmatwp`, `model.wigner`). To avoid the *ab initio* | ||
| step, here we use a nearest-neighbor model instead, which can be created with | ||
| `make model` or `python3 model.py`. | ||
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| 2. Based on these data, we can build a supercell model and set up the driver | ||
| with `make driver` or `python3 driver.py`. This will create files with the | ||
| driver object (`driver.pickle`) and initial ionic positions (`driver.xyz`). | ||
| Note that the dummy `driver.xyz` required for testing will be overwritten. | ||
| Git will show the file as modified (or deleted after running `make clean`). | ||
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| 3. Now we are ready to run i-PI and the driver, which will communicate via a | ||
| Unix domain socket, and perform the optimization with `make run`. This will | ||
| start i-PI in the background, wait until it is ready, and start the driver | ||
| with `i-pi-driver-py -u -m elphmod -o driver.pickle`. i-PI will output the | ||
| potential energies (`run.out`), positions (`run.pos_0.xyz`), and forces | ||
| (`run.for_0.xyz`) for all steps. | ||
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| 4. Finally, we can view the trajectory with `make plot` or `python3 plot.py`. | ||
| This should open an interactive figure and finally create `plot.pdf`, where | ||
| arrows indicate atomic displacements. Since we have used a simplistic model, | ||
| the periodic lattice distortion differs from the expected 3-by-3 pattern. | ||
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| Note that saving the driver to an intermediate file `driver.pickle` has two | ||
| advantages: First, when running it through `i-pi-driver-py`, only a single | ||
| parameter (the filename) has to be specified on the command line, rather than | ||
| all details of the flexible setup in `driver.py`. Second, setting up the driver | ||
| can be quite time consuming, so it is more efficient to do this only once when | ||
| launching it multiple times later. | ||
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| It is alternatively possible to run the driver through the module `ipi._driver`, | ||
| which is however only available if i-PI has been installed using `setuptools`, | ||
| e.g., through `pip`. This can be tested with `make run2` or `python3 run.py`. |
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| #!/usr/bin/env python3 | ||
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| """See [documentation](https://janberges.github.io/elphmod/modules/md.html).""" | ||
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| import elphmod | ||
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| el = elphmod.el.Model("model", rydberg=True) | ||
| ph = elphmod.ph.Model("model.ifc", divide_mass=False) | ||
| elph = elphmod.elph.Model("model.epmatwp", "model.wigner", el, ph, divide_mass=False) | ||
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| driver = elphmod.md.Driver( | ||
| elph, | ||
| nk=(12, 12), | ||
| nq=(2, 2), | ||
| supercell=(9, 9), | ||
| kT=0.02, | ||
| f=elphmod.occupations.marzari_vanderbilt, | ||
| n=1.0, | ||
| ) | ||
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| driver.kT = 0.005 | ||
| driver.f = elphmod.occupations.fermi_dirac | ||
| driver.random_displacements() | ||
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| driver.save("driver.pickle") | ||
| driver.to_xyz("driver.xyz") |
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| @@ -0,0 +1,5 @@ | ||
| 3 | ||
| # CELL{H}: 6.3116853 -3.15584265 0 0 5.466079812 0 0 0 28.34589207 | ||
| Ta 0.000000000 3.644053207 0.000000000 | ||
| S 3.155842650 1.822026604 2.834589207 | ||
| S 3.155842650 1.822026604 -2.834589207 |
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| Original file line number | Diff line number | Diff line change |
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| <simulation> | ||
| <output prefix='run'> | ||
| <properties stride='1' filename='out'>[step, potential]</properties> | ||
| <trajectory stride='1' filename='pos'>positions</trajectory> | ||
| <trajectory stride='1' filename='for'>forces</trajectory> | ||
| </output> | ||
| <ffsocket name='elphmod' mode='unix' pbc='false'> | ||
| <address>localhost</address> | ||
| </ffsocket> | ||
| <system> | ||
| <initialize nbeads='1'> | ||
| <file mode='xyz'>driver.xyz</file> | ||
| </initialize> | ||
| <forces> | ||
| <force forcefield='elphmod'></force> | ||
| </forces> | ||
| <motion mode='minimize'> | ||
| <optimizer mode='bfgs'></optimizer> | ||
| <fixcom>True</fixcom> | ||
| </motion> | ||
| </system> | ||
| </simulation> |
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