BDF User's guide

Insert introduction of BDF module at here.

How to run BDF

To run BDF, you can write a shell script named "run.sh" with following content,

 #!/bin/bash
 # Set BDF home directory
 export BDFHOME=~/work/0.5.dev

 # run BDF driver with input file $1
 $BDFHOME/sbin/bdfdrv.py -r $1

For example, you can copy the file named "$BDFHOME/Tests/input/test002.inp" to a work directory. Then, you write done the shell script and store it in you work directory. To evoke BDF calculation, you just use command

$./run.sh test001.inp

The output will be printed on standard output. Thus, it is better to redirect output to a file.

$./run.sh test001.inp > test001.out

Some tips to run BDF

 1. There are a lot of testing inputs saved in directory of $BDFHOME/Tests/input.
 2. BDF driver assume input file has the name *.inp. Thus, you can run BDF with command
    $./run.sh test001
 3. If BDF is compiled with OpenMP supporting, you can can set OpenMP environmental variables in running script. For example,
    export OMP_NUM_THREADS=4
    export OMP_STACKSIZE=1024M
 4. You can use shell command in BDF input files. For example, you can backup HF canonical orbitals after SCF calculation.
     $SCF
     $END
     %cp $BDF_WORKDIR/$BDFTASK.scforb $BDF_WORKDIR/myscforb.bak

BDF Flowchat

Input style

Environmental variables used in BDF

There are some important environmental variables used in BDF.

  1.BDF_WORKDIR  - Work directory used in running BDF program.   
  2.BDF_TMPDIR     -  Scratch directory used in running BDF program. This directory can be removed after the calculation.
  3.BDFTASK           - Task name of a BDF work.

BDF modules

compass - Molecule geometry and basis set preprocess.

drt - Generate DRTs in GUGA.

grad - Gradient.

mcscf - Multi-configuration self-consistent-field program

mp2 - MP2 program

mrci - Multi-reference configuration interaction program.

localmo - Localization of molecule orbital.

scf - Self-consistent-field program.

tddft - Time dependent density functional program.

vgmfci - electron-nucleus mean field configuration interaction program.

xuanyuan - 1e and 2e integrals program.

genfrag - Generate or optimize fragments and fragments pairs in Local orbital based Frag-MP2/CCSD.

expandmo - Expand molecular orbital from small basis set to large basis set.

resp - Module for response properties based on HF and DFT

QM/MM calculation

External charge -- Input point charges. A file named $BDFTASK.extcharg should be prepared. Here is an example.

H2O.inp

$COMPASS
Title
water molecule in backgroud of exteral charges
Basis
6-31g
Geometry
O   0.000000   0.000000   0.106830
H   0.000000   0.785178  -0.427319
H   0.000000  -0.785178  -0.427319
End Geometry
Extcharge    # required if external charge exists.
point        # required if external charge exists. "point" specifies the type of external charge is point charge.                                                                                                                                        
Check
Skeleton
$END

$XUANYUAN
direct
schwarz
$END

$SCF
RHF
$END

H2O.extcharge

External charge, Gaussian charge   # title line
6                # number of point charges. Next six lines are label, charge, x,y,z coordinates. Unit: angstrom(default)
C1     -0.732879     0.000000     5.000000     0.114039 
C2      0.366440     0.000000     5.780843    -0.456155 
C3      0.366440     0.000000     4.219157    -0.456155
C4     -0.732879     0.000000     10.00000     0.114039 
C5      0.366440     0.000000     10.78084    -0.456155 
C6      0.366440     0.000000     9.219157    -0.456155

Another example

External charge, Gaussian charge   # title line
6    Bohr                                               # number of point charges, Unit: Bohr
C1     -0.732879     0.000000     5.000000     0.114039 
C2      0.366440     0.000000     5.780843    -0.456155 
C3      0.366440     0.000000     4.219157    -0.456155
C4     -0.732879     0.000000     10.00000     0.114039 
C5      0.366440     0.000000     10.78084    -0.456155 
C6      0.366440     0.000000     9.219157    -0.456155

Useful tools

bdffrag