params - dictionary, containing a set of the key - value pairs

Because the function delivers the main NA-MD functionaliy of the PYXAID, the parameters will be discussed in a bit more details than for other functions of the distribution, on a separate page.

params - dictionary, containing a set of the key - value pairs

key - a string defining the key the value of which we want to extract from the dictionary

default - the default value corresponding to the key given, in the case if dictionary does not define it

typ - a string defining the data type of value corresponding to given key. The parameter 'default' must be of this type.
Allowed values:

• "i" - for extracting integer values
• "s" - for extracting string values
• "f" - for extracting floating-point values

runMD.runMD(...)

...

							params = {"EXE_EXPORT":"path_to_my_exe", dt:1.0, minband:1, maxband:10 } # define dictionary of parameters

							dt = get_value(params,"dt","1.0","f") # extract the value of variable params["dt"] and convert it to floating point type
							

params - dictionary, containing a set of the key - value pairs determining the details of calculations

• "NP" - integer, specifying on how many CPUs to run the electronic structure calculations (with the QE code). Default value = 1
• "EXE" - string, specifying the path the quantum-mechanical driver (pw program of QE package). Default value = ""
• "EXE_EXPORT" - string, specifying the path of the post-processing utility to transform the wavefunction to the text format (pw_export program of QE package). Default value = ""
• "start_indx" - integer, specifying the index of the starting MD trajectory point used for electronic Hamiltonian computations. Default value = 0
• "stop_indx" - integer, specifying the index of the final MD trajectory point used for electronic Hamiltonian computations. Default value = 1
• "dt" - real number, specifying the nuclear time step (in fs) used to produce MD trajectory. Default value = 1.0
• "pp_type" - string, specifying the type of the pseudo-potential(PP) to be employed in electronic structure calculations. Default value = "NC" - norm-conserving PP. Currently is not actually used.
• "wd" - string, specifying the path (relatively to the directory from which the function is called) to the directory where all calculations will be performed (working directory). This directory will be created, if it does not exist yet. Default value = "wd"
• "rd" - string, specifying the path (absolute!!!) to the directory where all results (Ham_ files, Hprime_ files, etc.) will be collected (results directory). This directory must already be created by the user. Default value = same as for "wd"
• "minband" - integer, specifying the index (starting from 1, not to exceed the number of bands used in scf calculations) of the minimal KS orbital to be included in the basis set of adiabatic KS (one-electron) states for which the Ham_ and Hprime_ files to be computed, including it. Default value = 1
• "maxband" - integer, specifying the index (starting from 1, not to exceed the number of bands used in scf calculations) of the maximal KS orbital to be included in the basis set of adiabatic KS (one-electron) states for which the Ham_ and Hprime_ files to be computed, including it. Default value = 2. Together with "minband" defines the dimensionality of the one-electron (KS basis) Hamiltonian matrix: maxband - minband + 1. Thus, for the default values of maxband = 2 and minband = 1 the electronic Hamiltonian is a 2 x 2 matrix, computed using the KS wavefunctions for the bands numbered 1 and 2, where 1 - is the first band (MO) given by QE code.
• "nocc" - integer, specifying the index (starting from 1, not to exceed the number of bands used in scf calculations) of the occupied KS orbital. Default value = 1. Together with default values for "minband" and "maxband" this corresponds to one occupied orbital (index 1) and one virtual orbital (index 2).
• "nac_method" - integer, specifying the type of an ad hoc NAC correction method.
  Available values:
  
  • 0 - no correction, NAC is computed as prescribed by Hammess-Schiffer and Tully[1]. See details in the PYXAIS paper.
  • 1 - use the NAC and band gap correction as described in our work (to be published).
  Default value = 0.
• "prefix0" - string, specifying the prefix for the files containing the input files for the electronic structure calculations used in this step. This is for the case when params["nac_method"] = 0 or params["nac_method"] = 1. Default value = "x0.scf". The prefix only defines the part of the input file, the full name of the input file also contains the integer that enumerates the MD trajectory point and the suffix - ".in". In other words, for the MD configuration 10 (this value must be between "start_indx" and "stop_indx" defined above) the input file will look like "x0.scf.10.in". Note that this file must be present in the directory from which the runMD2() function is called (current working directory).
• "prefix1" - similarly to "prefix0", but is used only if params["nac_method"] = 1. Default value = "x1.scf".
• "wfc_preprocess" - string, specifying how to process (transform) the wavefunction read from the raw wavefunction file (e.g. in "../curr0/x0.export/wfc.1") before using it to compute non-adiabatic couplings.
  Available values:
  
  • "normalize" - normalize all KS orbitals read from wfc. file to unity. Because such wfc is only pseudized one (unless this was excplicitly performed by the pw_export program), the KS orbitals will neither be orthogonal to each other nor they will be normalized. With this preprocessing option we help to make sure that they are at least normalized (this condition is used in derivation of the numeriacal expression for the NAC given by Hammess-Schiffer and Tully[1]). Still, KS orbitals may be non-orthogonal (but for the relatively large systems such non-orthogonality is relatively small)
  • "complete" - needed if the calculations are performed at the gamma-point. In this case only a half or the wavefunction is stored to save space. The other half (except for one point at the origin g = (0,0,0)) is obtained by complex conjugation of the first part due to symmetry: c(g) = c*(-g). So with this option we restore the full wavefunction before it is used to compute Hamiltonian matrix elements in the KS basis (Ham_ files) and other related quantities (such as Hprime_ files).
  • "restore" - as it has already be mentioned above, the originally produced (pseudized) KS orbitals are not orthogonal. With this option we "uproject" the pseudized wavefunctions to produce the true, "all-electron" wavefunctions (see out NAC correction paper for details). This ensures that the wavefunctions are orthogonal and normalized before we compute NACs and other related properties
  Default value = "restore".
• "do_complete" - integer, specifying if the wavefunction must be completed (see "complete" option to "wfc_preprocess" key) before it is restored (see "restore" option to "wfc_preprocess" key).
  Available values:
  
  • 0 - do not complete, restore the wavefunction straight ahead from what has been read
  • 1 - complete the wavefunction first, then restore the all-electron wavefunction from the restored pseudized one. This is needed if the gamma-trick is used, otherwise there may be problems in diagonalization procedures
  Default value = 1.
• "compute_Hprime" - integer, specifying if the transition dipole moments (Hprime_ files) are to be computed (along 3 directions) in addition to the Hamiltonian matrix elements (Ham_ files).
  Available values:
  
  • 0 - do not compute Hprime_ files
  • 1 - compute Hprime_ files
  Default value = 0.

level 3 codes

runMD.get_value(...)

pyxaid_core.wfc - class

pyxaid_core.wfc.QE_read_acsii_index(...)

pyxaid_core.wfc.QE_read_acsii_wfc(...)

pyxaid_core.wfc.normalize()

pyxaid_core.wfc.complete()

pyxaid_core.wfc.restore(...)

pyxaid_core.wfc.QE_read_acsii_grid(...)

pyxaid_core.wfc.compute_Hprime(...)

pyxaid_core.ham(...)

...