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## page was renamed from User Guide
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#format wiki
#language en
#Please change following line to BDF module name

= BDF User's guide =
<<TableOfContents(4)>>

{{{
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 ==

{{attachment:bdf_module_chart.jpg||width=640,align="middle"}} 

== 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, Point 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, Point 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
}}}

== PCM solver ==
To use PCM in BDF, you need add PCMSOLVER in SCF input. Then a pcminput section is required if you would like to change the default parameters in PCM solver. For detail: please check  [[PCMinput]] parameters.
{{{
$SCF
...
PCMSOLVER   # require PCM module
$END

&PCMINPUT   # PCM input
Solvent
   Chloroform  #  Set solvent as CHCl3
&END

}}}

== Useful tools ==
[[bdffrag]]