mirror of https://github.com/abinit/abinit.git
131 lines
6.8 KiB
Markdown
131 lines
6.8 KiB
Markdown
# The aTDEP utility
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The Temperature Dependent Effective Potential (TDEP) method
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has been developped by O. Hellman *et al.* [[cite:Hellman2011]],
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[[cite:Hellman2013]], [[cite:Hellman2013a]] in 2011 and the aTDEP implementation
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in ABINIT has been performed and used for the first time in 2015 by
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J. Bouchet and F. Bottin [[cite:Bouchet2015]], [[cite:Bouchet2017]].
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* User guide (in a pdf format): [[pdf:aTDEP_Guide|aTDEP_Guide]]
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* Theory: [[pdf:aTDEP_Paper|aTDEP_Paper]] corresponding to the article [[cite:Bottin2020]]
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## Prerequisite and theory
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The approach used in this code is detailed in a publication dedicated to the development
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of all formula (see [[pdf:aTDEP_Paper|aTDEP_Paper]]). We strongly encourage all the users to carefully read
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this paper before beginning. All the vibrational, elastic and thermodynamic
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quantities computed by aTDEP are
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presented with the same writing conventions as the ones used in the output files of aTDEP.
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In the same manner, a comprehensive understanding of some ABINIT basic variables is also required
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in order to fill the input file and read the output file of aTDEP.
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In addition, this paper is also useful to understand
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the limitations and convergences which are inherent to the present method.
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These particular points are sometimes discussed in the
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article, with some references and illustrating examples.
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## The ABINIT computation
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To run aTDEP, a preliminary
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ABINIT simulation is needed. This one could be a molecular dynamic trajectory
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or a set of "ground state" calculations on specific configurations (representative of a given thermodynamic state).
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After that, all the configurations have to be merged:
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(i) in a single *NetCDF* file `HIST.nc` or (ii) in three separated *ASCII* files `fcart.dat`, `xred.dat` and
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`etot.dat` (forces in cartesian coordinates, positions in reduced coordinates, total energies in Ha),
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as they are written in the output file of ABINIT. In the later case, the 3 files can be built easily
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by concatenating in each one all the time steps or configurations (using `agrep` shell instruction, for example).
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## The aTDEP computation
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In a same manner as performed for ABINIT, the use of aTDEP is quite simple.
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One has just to execute `atdep` as follows:
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```sh
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atdep < input.files > log
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```
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with the `input.files` file containing 3 lines. The first one defines the input
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file, the second one is the *NetCDF* file (if present, see above) and the third one
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defines the root of all the output files:
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input.in
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HIST.nc
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output
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The detection of the `HIST.nc` file is performed at the beginning; so, if this
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one is absent, the code will automatically search the 3 `ASCII.dat` files.
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## The input files
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An example of a aTDEP calculation (in the special case where the *NetCDF* file `HIST.nc` is employed)
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can be found in [[test:v8_37]]. The 2 input files are
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given in the `tests/v8/Input` directory.
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Let us describe briefly this [[test:v8_37]] file:
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{% dialog tests/v8/Input/t37.abi %}
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The input file format is fixed. So:
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1. This file begins with a `NormalMode` or `DebugMode` keyword and finishes with `TheEnd` (all the lines after are not read).
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2. All the lines between `# Unit cell definition` and `# Optional inputs` are fixed.
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3. Between `# Optional inputs` and `TheEnd`, the format is free.
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More details:
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* The section `# Unit cell definition` defines the bravais lattice [[brav@atdep|brav]]
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(here, a simple cubic), the number of atoms in the unit cell [[natom_unitcell@atdep|natom_unitcell]]
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(here, 5 atoms), their reduced coordinates in the unit cell [[xred_unitcell@atdep|xred_unitcell]]
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(here, a perovskite) and the type of atoms in the unit cell [[typat_unitcell@atdep|typat_unitcell]]
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(here, one atom A, one atom B and 3 atoms C).
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* The section `# Supercell definition` defines the multiplicity of the
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supercell with respect to the unit cell multiplicity (here, it is a simple
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2x2x2 multiplication of the unit cell) and the temperature of the system
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temperature(here, 495.05 K).
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* The section `# Computation details` defines the range [[nstep_max@atdep|nstep_max]]...[[nstep_min@atdep|nstep_min]]
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of time steps or configurations (here, 100 time steps) and the
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cutoff radius for the pair interactions [[rcut@atdep|Rcut]] (here, all the interaction pairs
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with a bond length larger than 7.426 bohr will not be considered).
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* The section `# Optional inputs` can define a large number of optional
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keywords (here [[ngqpt2@atdep|ngqpt2]] defining the q-point grid for the vDOS integration
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is set to 2 2 2 in order to have a test sufficiently fast, which means that
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all the thermodynamic quantities have no sense.)
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All the input variables are defined in the `aTDEP` section of the input variables description.
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Note that some input variables, not defined in the `input.in` file, are obtained
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from the `HIST.nc` file. In particular, the features of the supercell.
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<sub><sup>TODO: Explain the extra input variables when the 3 ASCII files are employed.</sup></sub>
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## The output files
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A large number of output files are obtained after an execution of aTDEP.
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{% dialog tests/v8/Refs/t37.abo %}
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{% dialog tests/v8/Refs/t37omega.dat %}
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{% dialog tests/v8/Refs/t37thermo.dat %}
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1. `*.abo` is the main output file. It includes an echo of the input variables,
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some intermediary results, the definition of the various shells of interaction,
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the second order IFCs for all the atoms in each shell, the elastic constants and moduli,
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the energy of the model...
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2. `*omega.dat` contains the dispersion of phonon frequencies (in meV) along a path in the Brillouin Zone.
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3. `*thermo.dat` lists all the thermodynamic quantities obtained by considering
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the system as a quantum harmonic crystal: specific heat, vibrational
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energy, entropy and free energy. It also gives all these contributions as a
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function of temperature in the harmonic approximation.
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4. `sym.dat` details all the symmetry operations of the bravais lattice,
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5. `qpt.dat` defines the q-point grid used to compute the phonon frequencies
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contained in the `omega.dat` file.
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6. `xredaverage.xyz` includes the ideal and average positions in the supercell.
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7. `Indym*.dat` contain all the symmetry relations between one or two atoms
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in the unit cell or the supercell.
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8. `vdos.dat` displays the vibrational density of states (in meV).
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9. `dij.dat` lists the dynamical matrices for a particular set of q-points.
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10. `etotMDvsTDEP2.dat` compares the MD trajectory with the one computed
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using the second order IFCs (these ones must be superimposed, as much
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as possible).
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11. `fcartMDvsTDEP2.dat` plots the MD forces wrt the forces computed using
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the second order IFCs (the cloud of points must be closer to the first bisector).
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12. `eigenvectors.dat` lists all the eigenvectors for a particular set of q-points.
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13. `nbcoeff-phij.dat` shows how the number of IFC coefficients are reduced (for each shell and each symmetry).
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14. ...
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