This chapter describes how to perform a single-point calculation of amino acid (glycine) using a single process.
ProteinDF writes a large number of large intermediate files with matrices/vectors on disk storage. Before starting actual calculations, create the following calculation directories:
.
Warning
The program may abnormally terminate if the intermediate files cannot be written properly. Before executing MPI parallel computation, make sure that the files can be properly written from all nodes.
Note
The user can execute ${PDF_HOME}/bin/pdfsetup to perform the operation above.
Create a text file with the following content, and save it under the name fl_Userinput:
>>>>MAIN
step-control = [create integral guess scf]
cut-value = 1.0e-10
scf-start-guess = harris
max-iteration = 100
method = nsp
method/nsp/electron-number = 40
method/nsp/occlevel = [ 1 - 20 ]
orbital-independence-threshold = 0.007
convergence/type = density
convergence/threshold = 1e-4
convergence/threshold-energy = 1e-5
scf-acceleration = damping
scf-acceleration/damping/damping-factor = 0.65
xc-potential = b3lyp
scf-acceleration/damping/damping-type = density_matrix
>>>>MOLECULE
geometry/cartesian/unit = angstrom
geometry/cartesian/input = {
N -1.888000 0.035000 -0.211000
H -1.766000 0.945000 0.189000
H -1.817000 0.099000 -1.205000
C -0.758000 -0.730000 0.287000
H -0.893000 -0.915000 1.372000
H -0.720000 -1.725000 -0.200000
C 0.529000 0.065000 0.064000
O 0.520000 1.294000 0.114000
O 1.742000 -0.451000 -0.186000
H 1.692000 -1.400000 -0.203000
}end
basis-set/orbital = {
H = "O-HYDROGEN (41) DZVP"
O = "O-OXYGEN (621/41) by FS"
C = "O-CARBON (621/41) by FS"
N = "O-NITROGEN (621/41) by FS"
}end
basis-set/density-auxiliary = {
H = "A-HYDROGEN (4,1;4,1) from deMon"
O = "A-OXYGEN (7/2;7/2) by FS"
C = "A-CARBON (7/2;7/2) by FS"
N = "A-NITROGEN (7/2;7/2) by FS"
}end
basis-set/exchange-auxiliary = {
H = "A-HYDROGEN (4,1;4,1) from deMon"
O = "A-OXYGEN (7/2;7/2) by FS"
C = "A-CARBON (7/2;7/2) by FS"
N = "A-NITROGEN (7/2;7/2) by FS"
}end
Note
Input files can be changed with a startup option of ProteinDF.
Configure the environment variable PDF_HOME appropriately, and execute ProteinDF (in serial mode).
% ${PDF_HOME}/bin/PDF.x
If the program terminates properly, the system returns to the command prompt.
The calculation results are output in files. The following shows an example of the output:
Note
The output file location can be changed with a startup option of ProteinDF.
The beginning of the output file shows the version of ProteinDF and the number of parallel processes (MPI process count, the number of OpenMP threads). Make sure that the calculation was performed as intended.
[0:2012/**/07 17:17:02:INFO] **************************************
[0:2012/**/07 17:17:02:INFO] ProteinDF version 20xx.x:xxxx (serial)
[0:2012/**/07 17:17:02:INFO]
[0:2012/**/07 17:17:02:INFO] OpenMP threads: 12
[0:2012/**/07 17:17:02:INFO]
The calculation is performed according to the procedure described in step_control. The output date is indicated at left in the log
===============================================
>>>> INTEGRAL
===============================================
>>>> Hpq
...
===============================================
>>>> GUESS
===============================================
...
===============================================
>>>> SCF
===============================================
Energy data are output in the Total Energy block.
------------------------------------------------
>>>> Total Energy
------------------------------------------------
Ts+Vn = -745.7264230071891689
E_J[Rho, Rho~] = 629.4907739256434525
E_J[Rho~,Rho~] = -311.1519936178789294
E_xc(pure) = -27.8222685895087842
E_K = -6.8830892822011522
E_nuclei = 179.8930288412503558
TE = -282.1999717298841688
------------------------------------------------
Other information, such as calculation size or cut off data, is output as needed.
When the calculation completes properly, the CPU time and elapsed time are output.
************************************************
ProteinDF successful completion
CPU_TIME: 3454 sec
ELAPS_TIME: 542 sec
************************************************