mirror of https://gitlab.com/QEF/q-e.git
377 lines
17 KiB
Plaintext
377 lines
17 KiB
Plaintext
*** FILE AUTOMATICALLY CREATED: DO NOT EDIT, CHANGES WILL BE LOST ***
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------------------------------------------------------------------------
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INPUT FILE DESCRIPTION
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Program: all_currents.x / QEHeat / Quantum ESPRESSO (version: 7.3)
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------------------------------------------------------------------------
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Program to compute energy current given the atomic configuration and the velocities of the atoms.
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Note that a very small conv_thr must be given in the ELECTRONS namelist, in the order of 1.D-11.
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The numerical derivative is very sensitive to this parameter and to "delta_t". Careful convergence
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tests are needed. Note that if too relaxed values are chosen, the result can depend on the algorithm
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used to diagonalize the hamiltonian a lot (the 4th/3rd digit can be wrong). Options that allows
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estimating the variance are provided, to reinitialize the wavefunctions and repeat each step many
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times ( "n_repeat_every_step" "re_init_wfc_1" "re_init_wfc_2" "re_init_wfc_3" ).
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Performance of the calculation can be tuned a little bit with the parameters "ethr_small_step"
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and "ethr_big_step", that can avoid the waste of some iterations in the diagonalization of the
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hamiltonian in the first scf step of every scf calculation (the program does 2 scf for each step).
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Note that in order to read atomic velocities, in the namelist CONTROL you must set calculation='md',
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and in the namelist IONS you must set ion_velocities='from_input'. Algorithm for computing finite
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difference derivatives can be set with the option "three_point_derivative" .
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This program implements
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Marcolongo, A., Umari, P. & Baroni, S.
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Microscopic theory and quantum simulation of atomic heat transport.
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Nature Phys 12, 80-84 (2016). https://doi.org/10.1038/nphys3509
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and was originally written by Aris Marcolongo in 2014 at SISSA for his PhD thesis
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( https://iris.sissa.it/handle/20.500.11767/3897 )
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The all_current driver program was rewritten from scratch by Riccardo Bertossa at SISSA in 2020.
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Other contributions are from Davide Tisi (SISSA), Loris Ercole (SISSA - EPFL ) and Federico Grasselli (SISSA).
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Details of the implementation are discussed in
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Marcolongo, Bertossa, Tisi, Baroni, https://arxiv.org/abs/2104.06383 (2021)
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All the namilist but "ENERGY_CURRENT" are the same as the program pw.x
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Structure of the input data:
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===============================================================================
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&ENERGY_CURRENT
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...
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/
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&CONTROL
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MUST SET calculation='md'
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...
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/
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&SYSTEM
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...
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/
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&ELECTRONS
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you may want startingwfc = 'random' (for better standard deviation estimation)
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...
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/
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[ &IONS
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MUST SET ion_velocities='from_input'
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...
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/ ]
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[ &CELL
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...
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/ ]
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ATOMIC_SPECIES
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X Mass_X PseudoPot_X
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Y Mass_Y PseudoPot_Y
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Z Mass_Z PseudoPot_Z
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ATOMIC_POSITIONS { alat | bohr | crystal | angstrom | crystal_sg }
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X 0.0 0.0 0.0 {if_pos(1) if_pos(2) if_pos(3)}
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Y 0.5 0.0 0.0
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Z O.0 0.2 0.2
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ATOMIC_VELOCITIES
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X 0.0 0.0 0.0
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Y 0.5 0.0 0.0
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Z O.0 0.2 0.2
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K_POINTS { gamma }
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if (gamma)
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nothing to read
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[ CELL_PARAMETERS { alat | bohr | angstrom }
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v1(1) v1(2) v1(3)
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v2(1) v2(2) v2(3)
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v3(1) v3(2) v3(3) ]
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========================================================================
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NAMELIST: &ENERGY_CURRENT
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+--------------------------------------------------------------------
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Variable: delta_t
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Type: REAL
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Default: 1.D0
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Description: Small timestep used to do the numerical derivative needed
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in order to compute some parts of the current. Note that is in the pw.x units.
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: file_output
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Type: CHARACTER
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Default: 'current_hz'
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Description: The program will write the output in "file_output" and "file_output" + '.dat'.
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In the latter file the format of the output is:
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NSTEP t_ps J_x J_y J_z Jele_x Jele_y Jele_z v_cm(1)_x v_cm(1)_y v_cm(1)_z ...
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where J_x, J_y, J_z are the three components of the DFT energy current,
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and can be easily post-processed by other external programs.
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Jele_* are the components of the electronic density current that may be used
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for decorrelation and better data analysis or for calculating the electric current.
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v_cm(1) ... v_cm(nsp) are the center of mass velocities for each atomic species.
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If "n_repeat_every_step" > 1, an additional file "file_output" + '.stat' is
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written with the following format:
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NSTEP t_ps mean(J_x) mean(J_y) mean(J_z) std(J_x) std(J_y) std(J_z)
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only one line per step is printed in this case (in the other output files you will
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find every calculation, also repeated ones). std is the standard deviation.
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: trajdir
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Type: CHARACTER
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Default: ''
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Description: Prefix of the cp.x trajectory. The program will try to open the files
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"trajdir" .pos and "trajdir" .vel
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The files, for n atoms, are formatted like this:
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NSTEP1 t_ps1
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x(1) y(1) z(2)
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. . .
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. . .
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. . .
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x(n) y(n) z(n)
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NSTEP2 t_ps2
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x(1) y(1) z(2)
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. . .
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. . .
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. . .
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x(n) y(n) z(n)
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...
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the order of the atomic types must be the same of the one provided in the input file.
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If the files are not found, only the positions and the velocities from the input file will be used.
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Note that the units are specified by the input file. The units of the velocities are the same of
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the positions with time in atomic units. If a cp.x trajectory is provided (see "vel_input_units" )
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a factor 2 can be used for the velocities.
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: vel_input_units
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Type: CHARACTER
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Default: 'PW'
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Description:
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This multiplies or not by a factor 2 the velocities given in the input.
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Available options are:
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'CP' :
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assume velocities are given in cp.x time units (thus multiplying by 2 the velocities)
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'PW' :
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assume velocities are given in pw.x time units
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: eta
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Type: REAL
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Default: 1.D0
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Description: Convergence parameter for Ewald-like sums
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: n_max
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Type: INTEGER
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Default: 5
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Description: Number of images in each direction used to converge some sums.
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: first_step
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Type: INTEGER
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Default: 0
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Description: The program will start with step istep >= "first_step".
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If greater than zero the input file's positions and velocities will be ignored.
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Note that this is not a sequential index but refers to the indexes reported in
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the input trajectory file. The index of 0 is assigned to the snapshot described
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in the input namelist file.
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: last_step
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Type: INTEGER
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Default: 0
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Description: The program will end with step istep <= "last_step".
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If 0, it will stop at the end of the trajectory file
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Note that this is not a sequential index but refers to the indexes reported in
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the input trajectory file.
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: step_mul
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Type: INTEGER
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Default: 1
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Description: The program will use the step only if
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MOD(step, "step_mul") == "step_rem".
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: step_rem
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Type: INTEGER
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Default: 0
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Description: The program will use the step only if
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MOD(step, "step_mul") == "step_rem".
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: ethr_small_step
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Type: REAL
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Default: 1.D-7
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Description: Diagonalization threshold after the small "delta_t" numerical derivative step.
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(the system changed a very little)
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: ethr_big_step
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Type: REAL
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Default: 1.D-3
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Description: Diagonalization threshold at the beginning of each step but the first,
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for wich the pw.x input value is used.
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: restart
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Type: LOGICAL
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Default: .false.
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Description: If true try to read "file_output" .dat and try to set "first_step" to the
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last step in the file + 1
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: subtract_cm_vel
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Type: LOGICAL
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Default: .false.
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Description: If true subtract from the velocities of all atoms for every step
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the center of mass velocity for each atomic type.
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It help to decorrelate a little the mass flux from the energy flux
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: add_i_current_b
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Type: LOGICAL
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Default: .false.
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Description: If true adds to the energy current a part that is correctly implemented only for cubic cells.
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This part is in the form of a sum over the atomic types of a constant time the center of mass velocity
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of the atomic type. It does not change the value of the thermal conductivity when the formula for the
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multicomponent case with the inverse of the Schur complement is used, and in the single component
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or solid case this is a non-diffusive contribution.
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: save_dvpsi
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Type: LOGICAL
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Default: .false.
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Description: If true allocate the space needed for saving the solution of the linear system betweew every calculation.
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The iterative algorithm will always start from there. By default it starts always from scratch.
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: re_init_wfc_1
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Type: LOGICAL
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Default: .false.
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Description: If true initializes, as specified in the ELECTRON namelist of the PW section, the wavefunctions
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before the first ground state calculation, then compute the charge density.
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Otherwise use the last calculated wavefunctions.
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: re_init_wfc_2
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Type: LOGICAL
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Default: .false.
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Description: If true initializes, as specified in the ELECTRON namelist of the PW section, the wavefunctions
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before the second ground state calculation, then compute the charge density.
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Otherwise use the last calculated wavefunctions.
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Note that if "three_point_derivative" is false, this has no effect.
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: re_init_wfc_3
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Type: LOGICAL
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Default: .false.
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Description: If true initializes, as specified in the ELECTRON namelist of the PW section, the wavefunctions
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before the third ground state calculation, then compute the charge density.
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Otherwise use the last calculated wavefunctions.
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: three_point_derivative
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Type: LOGICAL
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Default: .true.
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Description: If true calculates three ground stated: one at t - "delta_t" /2, one at t and one at t + "delta_t"/2.
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Obviously it needs more computer time, but the derivative should be better.
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: n_repeat_every_step
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Type: INTEGER
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Default: 1
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Description: Number of repetition of the full current calculation for each step. If > 1, the file "file_output" + '.stat'
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is written with some statistics. Note that if you don't specify at least "re_init_wfc_1" ,this may be useless.
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You may want to specify startingwfc = 'random' in the ELECTRONS namelist.
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: n_workers
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Type: INTEGER
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Default: 0
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Description: The calculation over all the trajectory is splitted in "n_workers" chunks. Then to run the code over all
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the trajectory you must run "n_workers" input files each one with a different "worker_id",
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from 0 to "n_workers" - 1 . Those inputs can run at the same time in the same folder. The "worker_id"
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will be appended to the outdir folder and to the "file_output" input variables, so you can safely run all
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the inputs in the same directory at the same time.
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: worker_id
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Type: INTEGER
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Default: 0
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Description: See "n_workers" variable
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+--------------------------------------------------------------------
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+--------------------------------------------------------------------
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Variable: continue_not_converged
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Type: LOGICAL
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Default: .false.
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Description: If it is not possible to find a ground state for a given frame of the trajectory, go to the next one.
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You will not find this step in the output file(s).
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+--------------------------------------------------------------------
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===END OF NAMELIST======================================================
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This file has been created by helpdoc utility on Fri Dec 15 09:57:20 CET 2023
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