Example Script???

[jdgayles16]

Can someone, write an example script of how to take a converge electronic *.nc file and begin to optimize the geometry with constraints on some atoms?

Code

device_configuration = nlread("CGsupergap05.nc", object_id="gID000")[0]

device_configuration = OptimizeGeometry(
        device_configuration,
        maximum_forces=0.05*eV/Ang,
        constraints=[0,1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,178,179,180,181,185,186,187,188,194,195,204,205,206,207,211,212,213,214,215,216,218,219,222,223,224,225,230,231,232,233,234,235,238,239,241,242,243,244,246,247,249,250,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404],
        trajectory_filename=None,
    )
nlsave('CGsupergap05.nc', device_configuration)
nlprint(device_configuration)

Another question: Between each optimization step is there an electronic convergence and if so, how are the criterion implemented.

[Nordland]

First of all I create a simple caluclation of a Methane molecule

Code: python

###############################################################
# Molecule configuration
###############################################################

# Define elements
elements = [Carbon, Hydrogen, Hydrogen, Hydrogen, Hydrogen]

# Define coordinates
cartesian_coordinates = [[ 0.      ,  0.      ,  0.      ],
                         [ 0.635288,  0.635288,  0.635288],
                         [-0.635288, -0.635288,  0.635288],
                         [-0.635288,  0.635288, -0.635288],
                         [ 0.635288, -0.635288, -0.635288]]*Angstrom

# Set up configuration
molecule_configuration = MoleculeConfiguration(
    elements=elements,
    cartesian_coordinates=cartesian_coordinates
    )

###############################################################
# Calculator
###############################################################
poisson_solver = FastFourierSolver()

calculator = LCAOCalculator(
    poisson_solver=poisson_solver,
    )

molecule_configuration.setCalculator(calculator)
nlprint(molecule_configuration)
molecule_configuration.update()
nlsave('scf.nc', molecule_configuration)

Using the script I setup the following scripter with a constraint on atom 1:

Code: python

configuration = nlread("scf.nc", object_id="gID000")[0]

configuration = OptimizeGeometry(
        configuration,
        maximum_forces=0.05*eV/Ang,
        constraints=[1],
        trajectory_filename=None,
    )
nlsave('relax.nc', configuration)
nlprint(configuration)

This works for me

[Anders Blom]

About the question, yes, each step in the optimization is a full self-consistent calculation with convergence criteria as specified as usual (tolerance etc).

[jdgayles16]

My script is almost identical to Nordland's second script yet i get the error seen in http://quantumwise.com/forum/index.php?topic=775.0 when i apply bias.

[Nordland]

We are working non-stop on a solution for this problem posted in this thread. It is only related to calculation of forces in MPI. So I guess that your script is flawless. Try running it without MPI, while we work on a solution.

[jdgayles16]

Thanks I will try that.

Jacob