diesel (c40b1)
Combined Quantum Mechanical and Molecular Mechanics Method
Based on DIESEL(GAMESS) in CHARMM
by Milan Hodoscek
(milan@helix.nih.gov,milan@cmm.ki.si)
Multi reference CI program DIESEL is connected to CHARMM
program in a QM/MM method. To obtain the integrals for input to
DIESEL program it is run from the GAMEss command.
* Description | Description of the gamess commands.
* Using | How to run GAMESS in CHARMM.
* Installation | How to install GAMESS in CHARMM environment.
* Status | Status of the interface code.
* Functionality | Functionality of the interface code.
Based on DIESEL(GAMESS) in CHARMM
by Milan Hodoscek
(milan@helix.nih.gov,milan@cmm.ki.si)
Multi reference CI program DIESEL is connected to CHARMM
program in a QM/MM method. To obtain the integrals for input to
DIESEL program it is run from the GAMEss command.
* Description | Description of the gamess commands.
* Using | How to run GAMESS in CHARMM.
* Installation | How to install GAMESS in CHARMM environment.
* Status | Status of the interface code.
* Functionality | Functionality of the interface code.
Top
The DIESEL QM potential is initialized with the GAMEss command.
[SYNTAX GAMEss]
GAMEss DIESel <int> <int> ... / for the rest of options » gamess /
In order to run DIESEL the standard GAMEss command must be used
with the added DIESel keyword. The integer numbers after this keyword
represent which energy is used in the CHARMM code for further
processing.
DIESEL is the program to perform multi reference CI calculations.
The DIESEL QM potential is initialized with the GAMEss command.
[SYNTAX GAMEss]
GAMEss DIESel <int> <int> ... / for the rest of options » gamess /
In order to run DIESEL the standard GAMEss command must be used
with the added DIESel keyword. The integer numbers after this keyword
represent which energy is used in the CHARMM code for further
processing.
DIESEL is the program to perform multi reference CI calculations.
Top
In order to run DIESEL with CHARMM one has provide separate
input files for GAMESS (» gamess ) and for DIESEL. The
information provided by GAMESS for DIESEL is the file which contains
MO one and two electron integrals. In order to obtain such integrals
one must specify RUNTYPE=MCSF in GAMESS control input. The follwing is
an example for water with 3-21g basis set:
$CONTRL COORD=UNIQUE NOSYM=1 ICHARG=0 SCFTYP=mcscf $END
$SYSTEM MEMORY=1400000 TIMLIM=100000 $END
$BASIS GBASIS=N21 NGAUSS=3 $END
$DET NCORE=1 NACT=6 NELS=8 $END
$MCSCF maxit=1 micit=1 $end
$DATA
$END
This produces the necessary moints file which can be read by DIESEL
input. This should be improved because we really don't need to run
MCSCF, especially because it is very memory demanding. But it is
currently the cheapest way to produce integrals over MO basis, without
extensive modification of GAMESS. ???
Typical DIESEL script would be for example:
#! /bin/sh
export DIESEL_EXE_DIR=/software/qc/diesel/1.14pre/Binaries/Intel
cat <<! >diesel.in
MOIntegralFileFormat = GAMESSC1
MOLCASRootDir = `pwd`
TempDir = `pwd`
NumberOfElectrons = 8
Multiplicities = { 1 }
IrReps = { 0 }
Roots = { 1 2 3 4 }
SelectionThresholds = { 1 1e-3 1e-5 }
MaxDavidsonIters = 40
MaxHamiltonStorageMem = 100MB
$DIESEL_EXE_DIR/diesel <diesel.in >diesel.out 2>diesel.prot.out
For complete information about DIESEL input see its own user's
guide. In order to provide the correct input files for GAMESS and
DIESEL one has to spcify the following ENVIronment comands in CHARMM
input script.
envi input "h2o.str"
envi output "h2o.gms"
envi punch "test.dat"
envi aoints "test.f8"
envi moints "test.f9"
envi dictnry "test.f10"
envi work15 "test.f15"
envi dasort "test.f20"
envi dafl30 "test.f30"
envi jkfile "test.f23"
envi casints "test.f13"
envi civectr "test.f12"
! For DIESEL
envi dieselscript "CI.job"
envi dieselout "dies.out"
DIESEL provides many energies (for various multiplicities and roots)
in the same run. In order to get one of them for further processing
(minimization for example; but be careful: no derivatives are
available so one has to do very costly numerical calculation) the two
integers after DIESEL keyword are for multiplicity and root,
respectively.
[NOTE: For complete example look at test/c28test/dieseltst.inp]
In order to run DIESEL with CHARMM one has provide separate
input files for GAMESS (» gamess ) and for DIESEL. The
information provided by GAMESS for DIESEL is the file which contains
MO one and two electron integrals. In order to obtain such integrals
one must specify RUNTYPE=MCSF in GAMESS control input. The follwing is
an example for water with 3-21g basis set:
$CONTRL COORD=UNIQUE NOSYM=1 ICHARG=0 SCFTYP=mcscf $END
$SYSTEM MEMORY=1400000 TIMLIM=100000 $END
$BASIS GBASIS=N21 NGAUSS=3 $END
$DET NCORE=1 NACT=6 NELS=8 $END
$MCSCF maxit=1 micit=1 $end
$DATA
$END
This produces the necessary moints file which can be read by DIESEL
input. This should be improved because we really don't need to run
MCSCF, especially because it is very memory demanding. But it is
currently the cheapest way to produce integrals over MO basis, without
extensive modification of GAMESS. ???
Typical DIESEL script would be for example:
#! /bin/sh
export DIESEL_EXE_DIR=/software/qc/diesel/1.14pre/Binaries/Intel
cat <<! >diesel.in
MOIntegralFileFormat = GAMESSC1
MOLCASRootDir = `pwd`
TempDir = `pwd`
NumberOfElectrons = 8
Multiplicities = { 1 }
IrReps = { 0 }
Roots = { 1 2 3 4 }
SelectionThresholds = { 1 1e-3 1e-5 }
MaxDavidsonIters = 40
MaxHamiltonStorageMem = 100MB
$DIESEL_EXE_DIR/diesel <diesel.in >diesel.out 2>diesel.prot.out
For complete information about DIESEL input see its own user's
guide. In order to provide the correct input files for GAMESS and
DIESEL one has to spcify the following ENVIronment comands in CHARMM
input script.
envi input "h2o.str"
envi output "h2o.gms"
envi punch "test.dat"
envi aoints "test.f8"
envi moints "test.f9"
envi dictnry "test.f10"
envi work15 "test.f15"
envi dasort "test.f20"
envi dafl30 "test.f30"
envi jkfile "test.f23"
envi casints "test.f13"
envi civectr "test.f12"
! For DIESEL
envi dieselscript "CI.job"
envi dieselout "dies.out"
DIESEL provides many energies (for various multiplicities and roots)
in the same run. In order to get one of them for further processing
(minimization for example; but be careful: no derivatives are
available so one has to do very costly numerical calculation) the two
integers after DIESEL keyword are for multiplicity and root,
respectively.
[NOTE: For complete example look at test/c28test/dieseltst.inp]
Top
Installation
------------
To obtain the program write to Michael Hanrath
(michael.hanrath@uni-koeln.de). Since the program is written in C++ it was
not practical to put it under CHARMM tree and compile them
together. CHARMM only knows how to execute the script which runs
DIESEL. DIESEL itsel is also just a driver for other programs. The
only input it needs from GAMESS is the one and two electron binary
file.
Installation
------------
To obtain the program write to Michael Hanrath
(michael.hanrath@uni-koeln.de). Since the program is written in C++ it was
not practical to put it under CHARMM tree and compile them
together. CHARMM only knows how to execute the script which runs
DIESEL. DIESEL itsel is also just a driver for other programs. The
only input it needs from GAMESS is the one and two electron binary
file.
Top
DIESEL/CHARMM interface status (February 2001)
- no derivatives in DIESEL
- C1 symetry
Problems to be solved:
- avoid running MCSCF
- cleanup the file name mess.
DIESEL/CHARMM interface status (February 2001)
- no derivatives in DIESEL
- C1 symetry
Problems to be solved:
- avoid running MCSCF
- cleanup the file name mess.
Top
Implementation
--------------
C++ is not very practical to compile with fortran programs so
are transformed to MO basis by GAMESS, CHARMM calls system routine to
run shell script for DIESEL. In it one has to specify the path to
DIESEL distribution.
Implementation
--------------
C++ is not very practical to compile with fortran programs so
are transformed to MO basis by GAMESS, CHARMM calls system routine to
run shell script for DIESEL. In it one has to specify the path to
DIESEL distribution.