Difference between revisions of "Explanations for C2H2 rt response input files"

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== &unit ==
+
== required and recommended variables ==
 +
 
 +
=== &unit ===
  
 
Mandatory: none
 
Mandatory: none
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For isolated systems (specified by <code>iperiodic = 0</code> in <code>&system</code>), the units of output files are basically Angstrom/eV/fs at the present.
 
For isolated systems (specified by <code>iperiodic = 0</code> in <code>&system</code>), the units of output files are basically Angstrom/eV/fs at the present.
  
−
== &calculation ==
+
=== &calculation ===
  
 
Mandatory: calc_mode
 
Mandatory: calc_mode
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For periodic systems (specified by <code>iperiodic = 3</code> in <code>&system</code>), both ground state and real time calculations should be carried out as a single task (<code>calc_mode = 'GS_RT'</code>).
 
For periodic systems (specified by <code>iperiodic = 3</code> in <code>&system</code>), both ground state and real time calculations should be carried out as a single task (<code>calc_mode = 'GS_RT'</code>).
  
−
== &control ==
+
=== &control ===
  
 
Mandatory: none
 
Mandatory: none
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'C2H2' defined by <code>surname = 'C2H2'</code> will be used in the filenames of output files.
 
'C2H2' defined by <code>surname = 'C2H2'</code> will be used in the filenames of output files.
  
−
== &parallel ==
+
=== &system ===
−
 
 
−
Mandatory: nproc_ob, nproc_domain, nproc_domain_s
 
−
 
 
−
&parallel
 
−
  nproc_ob = 1
 
−
  nproc_domain = 1,1,1
 
−
  nproc_domain_s = 1,1,1
 
−
/
 
−
 
 
−
For isolated systems (specified by <code>iperiodic = 0</code> in <code>&system</code>), these parameters must be set.
 
−
<code>nproc_ob = 1</code> indicates the number of MPI parallelization for orbitals.
 
−
<code>nproc_domain = 1,1,1</code> indicates the spatial division for orbitals in x,y,z directions.
 
−
<code>nproc_domain_s = 1,1,1</code> indicates the spatial divisions for Hartree potential in x,y,z directions.
 
−
 
 
−
Followings must be satisfied:
 
−
* <code>nproc_ob</code> * <code>nproc_domain(1)</code> * <code>nproc_domain(2)</code>* <code>nproc_domain(3)</code>=total number of processors
 
−
* <code>nproc_domain_s(1)</code> * <code>nproc_domain_s(2)</code>* <code>nproc_domain_s(3)</code>=total number of processors
 
−
* <code>nproc_domain_s(1)</code> is a multiple of <code>nproc_domain(1)</code>
 
−
* <code>nproc_domain_s(2)</code> is a multiple of <code>nproc_domain(2)</code>
 
−
* <code>nproc_domain_s(3)</code> is a multiple of <code>nproc_domain(3)</code>
 
−
 
 
−
== &system ==
 
  
 
Mandatory: iperiodic, al, nstate, nelem, natom
 
Mandatory: iperiodic, al, nstate, nelem, natom
  
−
  &system
+
&system
 
   iperiodic = 0
 
   iperiodic = 0
 
   al = 16d0, 16d0, 16d0
 
   al = 16d0, 16d0, 16d0
−
   nstate = 8
+
   nstate = 5
−
  nelec = 10
 
 
   nelem = 2
 
   nelem = 2
 
   natom = 4
 
   natom = 4
−
/
+
  nelec = 10
 +
/
  
 
<code>iperiodic = 0</code> indicates that isolated boundary condition is assumed.  
 
<code>iperiodic = 0</code> indicates that isolated boundary condition is assumed.  
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<code>nelem = 2</code> and <code>natom = 4</code> indicate the number of elements and the number of atoms in the system, respectively.
 
<code>nelem = 2</code> and <code>natom = 4</code> indicate the number of elements and the number of atoms in the system, respectively.
  
−
== &pseudo ==
+
=== &pseudo ===
  
 
Mandatory: pseudo_file, iZatom
 
Mandatory: pseudo_file, iZatom
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<code>Lmax_ps(1) = 1</code> and <code>Lloc_ps(1) = 1</code> indicate the maximum angular momentum of the pseudopotential projector and the angular momentum of the pseudopotential that will be treated as local, respectively.  
 
<code>Lmax_ps(1) = 1</code> and <code>Lloc_ps(1) = 1</code> indicate the maximum angular momentum of the pseudopotential projector and the angular momentum of the pseudopotential that will be treated as local, respectively.  
  
−
== &tgrid ==
+
=== &tgrid ===
  
 
Mandatory: dt, Nt
 
Mandatory: dt, Nt
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<code>nt=5000</code> specifies the number of time steps in the calculation.
 
<code>nt=5000</code> specifies the number of time steps in the calculation.
  
−
== &emfield ==
+
=== &emfield ===
  
 
Mandatory: ae_shape1
 
Mandatory: ae_shape1
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In output files, the polarizability and oscillator strength distribution, which is related to the imaginary part of the polarizability will be included.
 
In output files, the polarizability and oscillator strength distribution, which is related to the imaginary part of the polarizability will be included.
  
−
== &hartree ==
+
=== &atomic_coor ===
 +
 
 +
Mandatory: none
 +
 
 +
&atomic_coor
 +
'C'    0.000000    0.000000    0.599672  1
 +
'H'    0.000000    0.000000    1.662257  2
 +
'C'    0.000000    0.000000  -0.599672  1
 +
'H'    0.000000    0.000000  -1.662257  2
 +
/
 +
 
 +
List of atomic coordinates. Last column corresponds to kinds of elements.
 +
 
 +
== additional options ==
 +
 
 +
=== &parallel ===
 +
 
 +
Mandatory: none
 +
 
 +
&parallel
 +
  nproc_ob = 1
 +
  nproc_domain = 1,1,1
 +
  nproc_domain_s = 1,1,1
 +
/
  
−
Mandatory: num_pole_xyz(1:3) if meo=3 is specified
+
Followings are explanation of each variable.
 +
* <code>nproc_ob</code>: Number of MPI parallelization for orbitals that related to the wavefunction calculation.
 +
* <code>nproc_domain(3)'</code>: Number of MPI parallelization for each direction in real-space that related to the wavefunction calculation.
 +
* <code>nproc_domain_s(3)'</code>: Number of MPI parallelization for each direction in real-space that related to the electron density calculation.
 +
 
 +
Defaults are <code>0</code> for <code>nproc_ob</code>, <code>(0/0/0)</code> for <code>nproc_domain</code>, and <code>(0/0/0)</code> for <code>nproc_domain_s</code>. If users use the defauls, automatic proccess assignment is done. Users can also specify <code>nproc_ob</code>, <code>nproc_domain</code>, and <code>nproc_domain_s</code> manually. In that case, followings must be satisfied.
 +
* nproc_ob</code> * <code>nproc_domain(1)</code> * <code>nproc_domain(2)</code>* <code>nproc_domain(3)</code>=total number of processors
 +
* <code>nproc_domain_s(1)</code> * <code>nproc_domain_s(2)</code>* <code>nproc_domain_s(3)</code>=total number of processors
 +
* <code>nproc_domain_s(1)</code> is a multiple of <code>nproc_domain(1)</code>
 +
* <code>nproc_domain_s(2)</code> is a multiple of <code>nproc_domain(2)</code>
 +
* <code>nproc_domain_s(3)</code> is a multiple of <code>nproc_domain(3)</code>
 +
 
 +
=== &hartree ===
 +
 
 +
Mandatory: none
  
 
  &hartree
 
  &hartree
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* <code>meo=1</code>: Single pole is set.
 
* <code>meo=1</code>: Single pole is set.
 
* <code>meo=2</code>: Multipoles are set to the position of atoms.  
 
* <code>meo=2</code>: Multipoles are set to the position of atoms.  
−
* <code>meo=3</code>: Multipoles are set to the center of mass of electrons in cuboids. If <code>meo=3</code> is specified, <code>num_pole_xyz(1:3)</code> must be set. <code>num_pole_xyz(1:3)</code> are numbers of cuboids x-, y-, and z-directions.
+
* <code>meo=3</code>: Multipoles are set to the center of mass of electrons in cuboids.
 +
<code>num_pole_xyz(3)</code> are number of multipoles when <code>meo</code> is <code>3</code>. A default for <code>meo</code> is <code>3</code>, and defaults for <code>num_pole_xyz</code> are <code>(0,0,0)</code>. When default is set, number of multipoles is calculated automatically.
  
−
== &atomic_coor ==
+
=== &analysis ===
  
 
Mandatory: none
 
Mandatory: none
  
−
  &atomic_coor
+
  &analysis
−
'C'    0.000000    0.000000   0.599672  1
+
  out_psi = 'y'
−
'H'    0.000000    0.000000    1.662257  2
+
   out_dns = 'y'
−
'C'    0.000000    0.000000  -0.599672  1
+
   out_dos = 'y'
−
'H'   0.000000    0.000000  -1.662257  2
+
   out_pdos = 'y'
 +
   out_elf = 'y'
 
  /
 
  /
  
−
List of atomic coordinates. Last column corresponds to kinds of elements.
+
These namelists specify the output files.

Latest revision as of 10:08, 30 July 2017

required and recommended variables

&unit

Mandatory: none 

&units
  unit_length='Angstrom'
  unit_energy='eV'
  unit_time='fs'
/

This namelist specifies the unit system used in the "input" file. If you do not specify the units for some physical quantities, atomic unit will be used for those quantities.

For isolated systems (specified by iperiodic = 0 in &system), the units of output files are basically Angstrom/eV/fs at the present.

&calculation

Mandatory: calc_mode 

&calculation
  calc_mode = 'RT'
/

The variable calc_mode should be one of 'GS', 'RT', and 'GS-RT'. Note that the ground state ('GS') and real time ('RT') calculations should be done separately and sequentially for isolated systems (specified by iperiodic = 0 in &system). For periodic systems (specified by iperiodic = 3 in &system), both ground state and real time calculations should be carried out as a single task (calc_mode = 'GS_RT').

&control

Mandatory: none 

&control
  sysname = 'C2H2'
/

'C2H2' defined by surname = 'C2H2' will be used in the filenames of output files.

&system

Mandatory: iperiodic, al, nstate, nelem, natom 

&system
  iperiodic = 0
  al = 16d0, 16d0, 16d0
  nstate = 5
  nelem = 2
  natom = 4
  nelec = 10
/

iperiodic = 0 indicates that isolated boundary condition is assumed. al = 16d0, 16d0, 16d0 specifies the lengths of three sides of a rectangular parallelepiped where the grid points are prepared. nstate = 8 indicates the number of Kohn-Sham orbitals to be solved. nelec = 10 indicate the number of valence electrons in the system. nelem = 2 and natom = 4 indicate the number of elements and the number of atoms in the system, respectively.

&pseudo

Mandatory: pseudo_file, iZatom 

&pseudo
  iZatom(1)=6
  iZatom(2)=1
  pseudo_file(1)='C_rps.dat'
  pseudo_file(2)='H_rps.dat'
  Lmax_ps(1)=1
  Lmax_ps(2)=0
  Lloc_ps(1)=1
  Lloc_ps(2)=0
/

Information on pseudopotentials. iZatom(1) = 6 indicates the atomic number of the element 1. pseudo_file(1) = 'C_rps.dat' indicates the filename of the pseudopotential of element 1. Lmax_ps(1) = 1 and Lloc_ps(1) = 1 indicate the maximum angular momentum of the pseudopotential projector and the angular momentum of the pseudopotential that will be treated as local, respectively.

&tgrid

Mandatory: dt, Nt 

 & tgrid
  dt=1.25d-3
  nt=5000

/

dt=1.25d-3 specifies the time step of the time evolution calculations. nt=5000 specifies the number of time steps in the calculation.

&emfield

Mandatory: ae_shape1 

&emfield
  ae_shape1 = 'impulse'
  epdir_re1 = 0.d0,0.d0,1.d0
/

This is a sample to calculate polarizability and oscillator distribution from real-time electron dynamics calculations. Specifying ae_shape1 = 'impulse', a weak impulsive force is applied to the isolated matter at t=0 In output files, the polarizability and oscillator strength distribution, which is related to the imaginary part of the polarizability will be included.

&atomic_coor

Mandatory: none 

&atomic_coor
'C'    0.000000    0.000000    0.599672  1
'H'    0.000000    0.000000    1.662257  2
'C'    0.000000    0.000000   -0.599672  1
'H'    0.000000    0.000000   -1.662257  2
/

List of atomic coordinates. Last column corresponds to kinds of elements.

additional options

&parallel

Mandatory: none 

&parallel
  nproc_ob = 1
  nproc_domain = 1,1,1
  nproc_domain_s = 1,1,1
/

Followings are explanation of each variable.

  • nproc_ob: Number of MPI parallelization for orbitals that related to the wavefunction calculation.
  • nproc_domain(3)': Number of MPI parallelization for each direction in real-space that related to the wavefunction calculation.
  • nproc_domain_s(3)': Number of MPI parallelization for each direction in real-space that related to the electron density calculation.

Defaults are 0 for nproc_ob, (0/0/0) for nproc_domain, and (0/0/0) for nproc_domain_s. If users use the defauls, automatic proccess assignment is done. Users can also specify nproc_ob, nproc_domain, and nproc_domain_s manually. In that case, followings must be satisfied.

  • nproc_ob</code> * nproc_domain(1) * nproc_domain(2)* nproc_domain(3)=total number of processors
  • nproc_domain_s(1) * nproc_domain_s(2)* nproc_domain_s(3)=total number of processors
  • nproc_domain_s(1) is a multiple of nproc_domain(1)
  • nproc_domain_s(2) is a multiple of nproc_domain(2)
  • nproc_domain_s(3) is a multiple of nproc_domain(3)

&hartree

Mandatory: none 

&hartree
  meo = 3
  num_pole_xyz = 2,2,2
/

meo specifies the order of multipole expansion of electron density that is used to prepare boundary condition for the Hartree potential.

  • meo=1: Single pole is set.
  • meo=2: Multipoles are set to the position of atoms.
  • meo=3: Multipoles are set to the center of mass of electrons in cuboids.

num_pole_xyz(3) are number of multipoles when meo is 3. A default for meo is 3, and defaults for num_pole_xyz are (0,0,0). When default is set, number of multipoles is calculated automatically.

&analysis

Mandatory: none 

&analysis
  out_psi = 'y'
  out_dns = 'y'
  out_dos = 'y'
  out_pdos = 'y'
  out_elf = 'y'
/

These namelists specify the output files.

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