Hands-on Tutorials¶
Examples of QUICK input files can be found at QUICK_HOME/test and at this link.
For this tutorial we will use one water molecule as an example. The structure of a typical QUICK input is as follows.
HF BASIS=cc-pVDZ CUTOFF=1.0d-10 DENSERMS=1.0d-6 ENERGY <== Job command
<== Empty line
O -0.06756756 -0.31531531 0.00000000 |
H 0.89243244 -0.31531531 0.00000000 |<== Coordinates
H -0.38802215 0.58962052 0.00000000 |
Before running QUICK, make sure to set the necessary environmental variables as follows:
source $(installdir)/quick.rc
where installdir is the folder where QUICK was installed. This will add the directory that contains the QUICK executables to your path and also set an environment variable that points to the basis set directory. Depending on the installation, you may run QUICK as follows:
Serial version:
quick input.in
MPI version:
mpirun -np N quick.MPI input.in
where N is the number of processes that you wish to launch.
CUDA version:
quick.cuda input.in
MPI+CUDA version:
mpirun -np M quick.cuda.MPI input.in
where M (M <= number of GPUs) is the number of processes that you wish to launch. Each process will use one GPU. The GPUs can be distributed across multiple nodes, in which case you have to make sure that the correct number of processes are started on each node.
Now assume that we have successfully installed the CUDA version and set relevant the environment variables.
HF/DFT single point energy calculation¶
The typical keyword line in the input file for a HF/DFT calculation looks like this. Note that all keywords are separated by a single space. The order of the keywords is not relevant.
HF BASIS=cc-pVDZ CUTOFF=1.0d-10 DENSERMS=1.0d-6 ENERGY
^ ^ ^ ^ ^
| | | | |
| | | | Compute energy
| | | Density matrix convergence threshold
| | Integral cutoff
| Basis set
Hamiltonian
For DFT, we replace the HF hamiltonian with DFT and specify the functional name separated by a space. For example, we may ask for a B3LYP energy calculation with the following keyword line.
DFT B3LYP BASIS=cc-pVDZ CUTOFF=1.0d-10 DENSERMS=1.0d-6 ENERGY
^ ^ ^ ^ ^ ^
| | | | | |
| | | | | Compute energy
| | | | Density matrix convergence threshold
| | | Integral cutoff
| | Basis set
| Functional
Hamiltonian
Note that in the above line, we are using the NATIVE B3LYP functional. If we want to use the B3LYP functional through LIBXC, the keyword line should be specified as follows.
DFT LIBXC=HYB_GGA_XC_B3LYP BASIS=cc-pVDZ CUTOFF=1.0d-10 DENSERMS=1.0d-6 ENERGY
^ ^ ^ ^ ^ ^
| | | | | |
| | | | | Compute energy
| | | | Density matrix convergence threshold
| | | Integral cutoff
| | Basis set
| Functional
Hamiltonian
It is also possible to ask for exchange and correlation LIBXC functionals separately. For instance, if we use BLYP, the keyword line is specified as follows.
DFT LIBXC=GGA_X_B88,GGA_C_LYP BASIS=cc-pVDZ CUTOFF=1.0d-10 DENSERMS=1.0d-6 ENERGY
^ ^ ^ ^ ^ ^
| | | | | |
| | | | | Compute energy
| | | | Density matrix convergence threshold
| | | Integral cutoff
| | Basis set
| Functionals (Functional_1, Functional_2 separated by a comma)
Hamiltonian
NOTE: Currently, QUICK cannot handle more than two functionals at a time.
We now proceed with a HF single point energy calculation for a water molecule. Below is the input file, called water.in:
HF BASIS=cc-pVDZ CUTOFF=1.0d-10 DENSERMS=1.0d-6 ENERGY
O -0.06756756 -0.31531531 0.00000000
H 0.89243244 -0.31531531 0.00000000
H -0.38802215 0.58962052 0.00000000
Executing QUICK will give us a water.out file. Here is how to run using the CUDA version of QUICK.
quick.cuda water.in
The information reported in the water.out file are as follows. In the beginning of the output file, we can find information about job card and the GPU used for the calculation. The next section reports information from SAD initial guess. This will be followed by some information about the molecule such as input geometry, basis function information, etc.
=========== Molecule Input ==========
| TOTAL MOLECULAR CHARGE = 0 MULTIPLICITY = 1
| TOTOAL ATOM NUMBER = 3 NUMBER OF ATOM TYPES = 2
| NUMBER OF HYDROGEN ATOM = 2 NUMBER OF NON-HYDROGEN ATOM = 1
| NUMBER OF ELECTRONS = 10
-- INPUT GEOMETRY -- :
O -0.0676 -0.3153 0.0000
H 0.8924 -0.3153 0.0000
H -0.3880 0.5896 0.0000
-- DISTANCE MATRIX -- :
1 2 3
1 0.00000
2 1.81414 0.00000
3 1.81414 2.96300 0.00000
============== BASIS INFOS ==============
| BASIS FUNCTIONS = 25
| NSHELL = 12 NPRIM = 32
| JSHELL = 12 JBASIS = 32
Next we find information about the SCF iterations.
------------------------------------------------------------------------------------------------------------------------
NCYC ENERGY DELTA_E SCF_TIME DII_CYC DII_TIME O_TIME DIAG_TIME MAX_ERR RMS_CHG MAX_CHG
------------------------------------------------------------------------------------------------------------------------
1 -76.056050700 ------ 0.307 1 0.29 0.02 0.00 0.1775E+01 0.5918E-01 0.3593E+00
2 -75.980565869 -.754848E-01 0.010 2 0.00 0.01 0.00 0.2376E+00 0.1554E-01 0.1750E+00
3 -76.017433601 0.368677E-01 0.010 3 0.00 0.01 0.00 0.1050E+00 0.4979E-02 0.6042E-01
4 -76.025458827 0.802523E-02 0.010 4 0.00 0.01 0.00 0.2584E-01 0.1707E-02 0.1991E-01
5 -76.026128208 0.669381E-03 0.010 5 0.00 0.01 0.00 0.4594E-02 0.7144E-03 0.5988E-02
6 -76.026196776 0.685678E-04 0.010 6 0.00 0.01 0.00 0.9251E-03 0.1740E-03 0.1141E-02
7 -76.026199618 0.284200E-05 0.010 7 0.00 0.01 0.00 0.1452E-03 0.3909E-04 0.2857E-03
8 -76.026199744 0.126052E-06 0.010 8 0.00 0.01 0.00 0.3826E-04 0.7945E-05 0.7236E-04
9 -76.026199750 0.583184E-08 0.010 9 0.00 0.01 0.00 0.9753E-05 0.2119E-05 0.1871E-04
10 -76.026199750 0.388203E-09 0.011 10 0.00 0.01 0.00 0.2026E-05 0.4872E-06 0.4202E-05
------------------------------------------------------------------------------------------------------------------------
REACH CONVERGENCE AFTER 10 CYLCES
MAX ERROR = 0.202570E-05 RMS CHANGE = 0.487164E-06 MAX CHANGE = 0.420193E-05
-----------------------------------------------
This is followed by electronic, nuclear, and total energies.
ELECTRONIC ENERGY = -85.183315734
CORE_CORE REPULSION = 9.157115983
TOTAL ENERGY = -76.026199750
Finally, we find timing information about the calculation.
HF/DFT gradient calculation¶
For a HF/DFT gradient calculation input the ENERGY flag is replaced by GRADIENT. Our water example input is now modified as follows.
HF BASIS=cc-pVDZ CUTOFF=1.0d-10 DENSERMS=1.0d-6 GRADIENT
O -0.06756756 -0.31531531 0.00000000
H 0.89243244 -0.31531531 0.00000000
H -0.38802215 0.58962052 0.00000000
In the calculation output, we can find the gradient immediately after the SCF cycles and energy information, and before the timings. The above example will print the following gradient.
ANALYTICAL GRADIENT:
----------------------------------------
COORDINATE XYZ GRADIENT
----------------------------------------
1X -0.0675675652 0.0126073406
1Y -0.3153153341 0.0180535055
1Z 0.0000000000 -0.0000000303
2X 0.8924325081 -0.0049459616
2Y -0.3153153341 -0.0099345180
2Z 0.0000000000 0.0000000419
3X -0.3880221796 -0.0076370422
3Y 0.5896205650 -0.0080873988
3Z 0.0000000000 -0.0000000115
----------------------------------------
Finally, the timings section also shows gradient timings for 1e, 2e, and exchange correlation calculations.
HF/DFT geometry optimization¶
For HF/DFT geometry optimizations, we should specify the OPTIMIZE flag in the QUICK input. For instance, the geometry optimization input for our water molecule would be:
HF BASIS=cc-pVDZ CUTOFF=1.0d-10 DENSERMS=1.0d-6 OPTIMIZE
O -0.06756756 -0.31531531 0.00000000
H 0.89243244 -0.31531531 0.00000000
H -0.38802215 0.58962052 0.00000000
QUICK geometry optimization output will contain information of SCF, gradient, and cartesian coordinates for each optimization step. As in the gradient calculation, the analytical gradients will be printed out immediately after the SCF information.
ANALYTICAL GRADIENT:
----------------------------------------------------------------------------
VARIBLES OLD_X OLD_GRAD NEW_GRAD NEW_X
----------------------------------------------------------------------------
1X -0.0876252350 0.0000197070 0.0000066787 -0.0876309328
1Y -0.3438974485 0.0000305134 0.0000178110 -0.3439209444
1Z 0.0000002515 -0.0000000336 -0.0000000335 0.0000002992
2X 0.8793809511 -0.0000260952 0.0000050220 0.8793829892
2Y -0.2849281308 0.0000367010 0.0000272289 -0.2849766745
2Z -0.0000003515 0.0000000484 0.0000000483 -0.0000004202
3X -0.3550174280 0.0000168026 -0.0000012871 -0.3550285769
3Y 0.5874160803 -0.0000028098 0.0000193489 0.5873964801
3Z 0.0000001020 -0.0000000153 -0.0000000153 0.0000001238
----------------------------------------------------------------------------
Next we find information essential for the convergence of geometry optimization.
OPTIMIZATION STATISTICS:
ENERGY CHANGE = -0.9827189729E-08 (REQUEST= 0.10000E-05)
MAXIMUM GEOMETRY CHANGE = 0.4854368017E-04 (REQUEST= 0.18000E-02)
GEOMETRY CHANGE RMS = 0.1958922994E-04 (REQUEST= 0.12000E-02)
GRADIENT NORM = 0.1292934393E-04 (REQUEST= 0.30000E-03)
The cartesian coordinates of the molecular geometry on each optimization step are printed next.
OPTIMIZED GEOMETRY IN CARTESIAN
ELEMENT X Y Z
O -0.0876 -0.3439 0.0000
H 0.8794 -0.2850 -0.0000
H -0.3550 0.5874 0.0000
We can also find the energy of the minimum structure at the end of output, right before the timings are printed out.
HF/DFT energies and gradients in the presence of external point charges¶
In order to compute energies and gradients of molecular systems containing external point charges, we must include cartesian coordinates (in Angstroms), charges (in au.), and EXTCHARGES keyword in the input file. Below is an example input of a point charge gradient calculation for a system containing a single water molecule and 3 point charges.
DFT B3LYP BASIS=cc-pvDZ cutoff=1.0e-9 denserms=1.0e-6 GRADIENT EXTCHARGES
O -0.741530 1.752130 2.896280
H -1.111151 0.979769 3.352290
H -0.920500 2.036450 1.984040
<== Empty line
1.6492 0.0000 -2.3560 -0.8340
0.5448 0.0000 -3.8000 0.4170
0.5448 0.0000 -0.9121 0.4170
\___________________/ ^
^ |
| Charge
Cartesian coordinates
The total energy and nuclear gradients reported in the output of this calculation include the effect of point charges. In addition, QUICK will report point charge gradients next to nuclear gradients section in the output. The point charge gradient is the force exerted on the point charges due to the electric field of the molecular charge density (electron density plus nuclear charges).
Last updated by Madu Manathunga on 03/23/2021.