Navigation
SEARCH
TOOLBOX
LANGUAGES
Forum Menu

a molpro CCSD(t) calculation with BSSE correction and bond function input file to nwchem input

From NWChem

Viewed 185 times, With a total of 5 Posts
Jump to: navigation, search
Forum >> NWChem's corner >> Running NWChem

Just Got Here
Threads 1
Posts 4
12:31:09 AM PST - Mon, Feb 6th 2012
Hi,

I have been observing the evolution of NWChem for quite sometime
and really interested in the use NWChem for high level calculations in distributed cluster. And recently I'd started to try it.
As my first test, I want to compare the CCSD(t) energy calculation in molpro and NWChem.
The calculation here is to determine the molecular interaction between CO2 and N2O.
I have used the input file below for molpro calculation:

      • co2-n2o vdw

memory,200,m

geometry={
nosymm;
angstrom;
He
X 1 1.0
C 1 r0 2 90.0
X 3 1.0 1 90.0 2 b1
X 3 1.0 1 90.0 4 90.0
O1 3 rc 5 90.0 1 a1
O2 3 rc 5 90.0 6 180.0
X 1 r0 2 90.0 3 180.0
X 8 1.0 1 90.0 2 0.0
X 8 1.0 9 90.0 1 90.0
O3 8 r1 10 90.0 1 a2
N3 8 r2 10 90.0 11 180.0
N4 8 r3 10 90.0 11 180.0}

rc=1.162047
r1=1.113058
r2=0.072042
r3=1.199342
r0= 3.5000
a1= 60.0000
a2=120.0000
b1= 90.0000


basis={
default=avtz;
s,he,0.9,0.3,0.1;
p,he,0.9,0.3,0.1;
d,he,0.6,0.2;
f,he,0.3}

text,total energy for vdw complex
dummy he
hf
ccsd(t)
etot=energy

text,energy of co2
dummy he,o3,n3,n4
hf
ccsd(t)
en2o1=energy

text,energy of n2o
dummy he,c,o1,o2
hf
ccsd(t)
en2o2=energy

de=(etot-en2o1-en2o2)*tocm

show etot,en2o1,en2o2,de
---

Just clueless about how to make a workable nwchem input for it especially in BSSE and bond functions with He.

Appreciate your help very much.

best,
Lu Yunpeng

Just Got Here
Threads 1
Posts 4
5:57:39 AM PST - Mon, Feb 6th 2012
well, I finally got one input after reading through the user manual.
==================================================
echo
start molecule

title "CO2-N2O interaction, CCSD(T) calculation"
charge 0

geometry "CO2_N2O" units angstroms print xyz autosym
Bq                 0.00000000    0.00000000    0.00000000

C                  3.50000000    0.00000000    0.00000000

O                  2.91897650   -1.00636222    0.00000000

O                  4.08102350    1.00636222    0.00000000

O                 -4.05652900   -0.00000000   -0.96393650

N                 -3.46397900   -0.00000000    0.06239020

N                 -2.90032900   -0.00000000    1.03866064
end

basis sperical
 C library aug-cc-pvtz

 N library aug-cc-pvtz

 O library aug-cc-pvtz

 BqC library C aug-cc-pvtz

 BqN library N aug-cc-pvtz

 BqO library O aug-cc-pvtz

 Bq s

  0.9000   1.000000

 Bq s

  0.3000   1.000000

 Bq s

  0.1000   1.000000

 Bq p

  0.9000   1.000000

 Bq p

  0.3000   1.000000

 Bq p

  0.1000   1.000000

 Bq d

  0.6000   1.000000

 Bq d

  0.2000   1.000000

 Bq f

  0.3000   1.000000
end

bsse
mon oco 2 3 4
mon nno 5 6 7
end

SCF
 singlet

 rhf
end

tce
 scf

 ccsd(t)

 freeze core
end

ecce_print test.out

scratch_dir /scratch/NWCHEM

task tce energy
==========================================

But it can not run as I got the error information as following:


                    Input BSSE Module - Counter Poise Approach

                  --------------------------------------------



 geom_rtdb_load: not found or rtdb corrupt: geometry -> geometry

geom_rtdb_load: open geometies:  1

 1 geom_rtdb_load: "geometry" -> "geometry"

geom_rtdb_load: geometries in last accessed data base:  1

CO2_N2O

------------------------------------------------------------------------

bsse_input: no geometry load form rtdb        0

------------------------------------------------------------------------

------------------------------------------------------------------------

 current input line :

   44: bsse

------------------------------------------------------------------------

------------------------------------------------------------------------

There is an error related to the specified geometry

------------------------------------------------------------------------

For more information see the NWChem manual at

http://www.emsl.pnl.gov/docs/nwchem/nwchem.html




For further details see manual section:




0:0:bsse_input: no geometry load form rtdb:: 0
(rank:0 hostname:c27.cluster.spms.ntu.edu.sg pid:14116):ARMCI DASSERT fail. armci.c:ARMCI_Error():260 cond:0

So why the declaration in bsse does not work?

thanks,
Lu Yunpeng

  • Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
    Profile
    Send PM
Forum Regular
Threads 2
Posts 286
5:49:14 PM PST - Mon, Feb 6th 2012
If you <name> the geometry, you need to set the geometry you want to use. By default nwchem assumes a geometry with the default <name> "geometry", which is also chosen when the <name> is left blank. See:

<name> - user-supplied name for the geometry; the default name is geometry, and all NWChem modules look for a geometry with this name. However, multiple geometries may be specified by using a different name for each. Subsequently, the user can direct a module to a named geometry by using the SET directive (see the example in Section 5.7) to associate the default name of geometry with the alternate name.

I.e. in your case, you need to define:

  set geometry "CO2_N2O"

Or you simply remove the name.

Bert




Quote:Luyunpeng Feb 6th 12:57 pm
well, I finally got one input after reading through the user manual.
==================================================
echo
start molecule

title "CO2-N2O interaction, CCSD(T) calculation"
charge 0

geometry "CO2_N2O" units angstroms print xyz autosym
Bq                 0.00000000    0.00000000    0.00000000

C                  3.50000000    0.00000000    0.00000000

O                  2.91897650   -1.00636222    0.00000000

O                  4.08102350    1.00636222    0.00000000

O                 -4.05652900   -0.00000000   -0.96393650

N                 -3.46397900   -0.00000000    0.06239020

N                 -2.90032900   -0.00000000    1.03866064
end

basis sperical
 C library aug-cc-pvtz

 N library aug-cc-pvtz

 O library aug-cc-pvtz

 BqC library C aug-cc-pvtz

 BqN library N aug-cc-pvtz

 BqO library O aug-cc-pvtz

 Bq s

  0.9000   1.000000

 Bq s

  0.3000   1.000000

 Bq s

  0.1000   1.000000

 Bq p

  0.9000   1.000000

 Bq p

  0.3000   1.000000

 Bq p

  0.1000   1.000000

 Bq d

  0.6000   1.000000

 Bq d

  0.2000   1.000000

 Bq f

  0.3000   1.000000
end

bsse
mon oco 2 3 4
mon nno 5 6 7
end

SCF
 singlet

 rhf
end

tce
 scf

 ccsd(t)

 freeze core
end

ecce_print test.out

scratch_dir /scratch/NWCHEM

task tce energy
==========================================

But it can not run as I got the error information as following:


                    Input BSSE Module - Counter Poise Approach

                  --------------------------------------------



 geom_rtdb_load: not found or rtdb corrupt: geometry -> geometry

geom_rtdb_load: open geometies:  1

 1 geom_rtdb_load: "geometry" -> "geometry"

geom_rtdb_load: geometries in last accessed data base:  1

CO2_N2O

------------------------------------------------------------------------

bsse_input: no geometry load form rtdb        0

------------------------------------------------------------------------

------------------------------------------------------------------------

 current input line :

   44: bsse

------------------------------------------------------------------------

------------------------------------------------------------------------

There is an error related to the specified geometry

------------------------------------------------------------------------

For more information see the NWChem manual at

http://www.emsl.pnl.gov/docs/nwchem/nwchem.html




For further details see manual section:




0:0:bsse_input: no geometry load form rtdb:: 0
(rank:0 hostname:c27.cluster.spms.ntu.edu.sg pid:14116):ARMCI DASSERT fail. armci.c:ARMCI_Error():260 cond:0

So why the declaration in bsse does not work?

thanks,
Lu Yunpeng

Just Got Here
Threads 1
Posts 4
10:08:45 PM PST - Mon, Feb 6th 2012
thanks for your reply, Bert.

I have modified the input a bit more to just calculate only the total energy for CO2-N2O dimer.
===============================================
echo
start molecule

memory 7000 mb

ecce_print test.out

scratch_dir /scratch/NWCHEM

title "CO2-N2O interaction, CCSD(T) calculation"
charge 0

geometry units angstroms print xyz autosym
Bq                 0.00000000    0.00000000    0.00000000

C                  3.50000000    0.00000000    0.00000000

O                  2.91897650   -1.00636222    0.00000000

O                  4.08102350    1.00636222    0.00000000

O                 -4.05652900   -0.00000000   -0.96393650

N                 -3.46397900   -0.00000000    0.06239020

N                 -2.90032900   -0.00000000    1.03866064
end

basis spherical
 C library aug-cc-pvtz

 N library aug-cc-pvtz

 O library aug-cc-pvtz

 BqC library C aug-cc-pvtz

 BqN library N aug-cc-pvtz

 BqO library O aug-cc-pvtz

 Bq s

  0.9000   1.000000

 Bq s

  0.3000   1.000000

 Bq s

  0.1000   1.000000

 Bq p

  0.9000   1.000000

 Bq p

  0.3000   1.000000

 Bq p

  0.1000   1.000000

 Bq d

  0.6000   1.000000

 Bq d

  0.2000   1.000000

 Bq f

  0.3000   1.000000
end

tce
 scf

 ccsd(t)

 freeze core
end

task tce energy
=============================================

The job ran for a while, with the error information below:
createfile: failed ga_create size=*********

 available GA memory             3669922976  bytes

createfile: failed ga_create size=*********

------------------------------------------------------------------------

------------------------------------------------------------------------

 available GA memory             3669922976  bytes

createfile: failed ga_create size=*********

------------------------------------------------------------------------

------------------------------------------------------------------------

createfile: failed ga_create size=*********

------------------------------------------------------------------------

------------------------------------------------------------------------

 current input line :

    0:

------------------------------------------------------------------------

 available GA memory             3669738608  bytes

createfile: failed ga_create size=*********

------------------------------------------------------------------------

------------------------------------------------------------------------

 current input line :

 available GA memory             3669738608  bytes

createfile: failed ga_create size=*********

 current input line :

    0:

------------------------------------------------------------------------

------------------------------------------------------------------------

------------------------------------------------------------------------

For more information see the NWChem manual at

createfile: failed ga_create size=*********

------------------------------------------------------------------------

------------------------------------------------------------------------

 current input line :

    0:

------------------------------------------------------------------------

------------------------------------------------------------------------

------------------------------------------------------------------------

For more information see the NWChem manual at

http://www.emsl.pnl.gov/docs/nwchem/nwchem.html



------------------------------------------------------------------------

------------------------------------------------------------------------

 current input line :

    0:

------------------------------------------------------------------------

------------------------------------------------------------------------

------------------------------------------------------------------------

For more information see the NWChem manual at

http://www.emsl.pnl.gov/docs/nwchem/nwchem.html

 current input line :

    0:

------------------------------------------------------------------------

------------------------------------------------------------------------

------------------------------------------------------------------------

For more information see the NWChem manual at

http://www.emsl.pnl.gov/docs/nwchem/nwchem.html



------------------------------------------------------------------------

------------------------------------------------------------------------

For more information see the NWChem manual at

http://www.emsl.pnl.gov/docs/nwchem/nwchem.html




For further details see manual section:




7:7:createfile: failed ga_create size=:: 1662623641
    0:

------------------------------------------------------------------------

------------------------------------------------------------------------

------------------------------------------------------------------------

For more information see the NWChem manual at

http://www.emsl.pnl.gov/docs/nwchem/nwchem.html

------------------------------------------------------------------------

------------------------------------------------------------------------

 current input line : 

    0: 

------------------------------------------------------------------------

------------------------------------------------------------------------

http://www.emsl.pnl.gov/docs/nwchem/nwchem.html





For further details see manual section:
6:6:createfile: failed ga_create size=:: 1662623641


For further details see manual section:
3:3:createfile: failed ga_create size=:: 1662623641
(rank:3 hostname:c27.cluster.spms.ntu.edu.sg pid:17216):ARMCI DASSERT fail. armci.c:ARMCI_Error():260 cond:0




For further details see manual section:



(rank:7 hostname:c27.cluster.spms.ntu.edu.sg pid:17220):ARMCI DASSERT fail. armci.c:ARMCI_Error():260 cond:0


For further details see manual section:






------------------------------------------------------------------------

For more information see the NWChem manual at

http://www.emsl.pnl.gov/docs/nwchem/nwchem.html




For further details see manual section:




(rank:6 hostname:c27.cluster.spms.ntu.edu.sg pid:17219):ARMCI DASSERT fail. armci.c:ARMCI_Error():260 cond:0
4:4:createfile: failed ga_create size=:: 1662623641
(rank:4 hostname:c27.cluster.spms.ntu.edu.sg pid:17217):ARMCI DASSERT fail. armci.c
ARMCI_Error():260 cond:0
------------------------------------------------------------------------
5:5:createfile: failed ga_create size=:: 1662623641
(rank:5 hostname:c27.cluster.spms.ntu.edu.sg pid:17218):ARMCI DASSERT fail. armci.c
ARMCI_Error():260 cond:0
1:1:createfile: failed ga_create size=:: 1662623641
(rank:1 hostname:c27.cluster.spms.ntu.edu.sg pid:17214):ARMCI DASSERT fail. armci.c:ARMCI_Error():260 cond:0
2:2:createfile: failed ga_create size=:: 1662623641
(rank:2 hostname:c27.cluster.spms.ntu.edu.sg pid:17215):ARMCI DASSERT fail. armci.c:ARMCI_Error():260 cond:0
For more information see the NWChem manual at  http://www.emsl.pnl.gov/docs/nwchem/nwchem.html




For further details see manual section:




0:0:createfile: failed ga_create size=:: 1662623641
(rank:0 hostname:c27.cluster.spms.ntu.edu.sg pid:17213):ARMCI DASSERT fail. armci.c
ARMCI_Error():260 cond:0

The computation node I use has 8 processors and 62GB RAM.

What is going wrong there?

Just Got Here
Threads 1
Posts 4
12:02:48 AM PST - Tue, Feb 7th 2012
well, GA algorithm not working for this one, too big.

  • Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
    Profile
    Send PM
Forum Regular
Threads 2
Posts 286
10:48:07 AM PST - Tue, Feb 7th 2012
Try adding to the TCE block:

tilesize 10
attilesize 15
2eorb
2emet 14

This should reduce the memory footprint. How many basis functions is this calculation?

Bert





Quote:Luyunpeng Feb 7th 5:08 am
thanks for your reply, Bert.

I have modified the input a bit more to just calculate only the total energy for CO2-N2O dimer.
===============================================
echo
start molecule

memory 7000 mb

ecce_print test.out

scratch_dir /scratch/NWCHEM

title "CO2-N2O interaction, CCSD(T) calculation"
charge 0

geometry units angstroms print xyz autosym
Bq                 0.00000000    0.00000000    0.00000000

C                  3.50000000    0.00000000    0.00000000

O                  2.91897650   -1.00636222    0.00000000

O                  4.08102350    1.00636222    0.00000000

O                 -4.05652900   -0.00000000   -0.96393650

N                 -3.46397900   -0.00000000    0.06239020

N                 -2.90032900   -0.00000000    1.03866064
end

basis spherical
 C library aug-cc-pvtz

 N library aug-cc-pvtz

 O library aug-cc-pvtz

 BqC library C aug-cc-pvtz

 BqN library N aug-cc-pvtz

 BqO library O aug-cc-pvtz

 Bq s

  0.9000   1.000000

 Bq s

  0.3000   1.000000

 Bq s

  0.1000   1.000000

 Bq p

  0.9000   1.000000

 Bq p

  0.3000   1.000000

 Bq p

  0.1000   1.000000

 Bq d

  0.6000   1.000000

 Bq d

  0.2000   1.000000

 Bq f

  0.3000   1.000000
end

tce
 scf

 ccsd(t)

 freeze core
end

task tce energy
=============================================

The job ran for a while, with the error information below:
createfile: failed ga_create size=*********

 available GA memory             3669922976  bytes

createfile: failed ga_create size=*********

------------------------------------------------------------------------

------------------------------------------------------------------------

 available GA memory             3669922976  bytes

createfile: failed ga_create size=*********

------------------------------------------------------------------------

------------------------------------------------------------------------

createfile: failed ga_create size=*********

------------------------------------------------------------------------

------------------------------------------------------------------------

 current input line :

    0:

------------------------------------------------------------------------

 available GA memory             3669738608  bytes

createfile: failed ga_create size=*********

------------------------------------------------------------------------

------------------------------------------------------------------------

 current input line :

 available GA memory             3669738608  bytes

createfile: failed ga_create size=*********

 current input line :

    0:

------------------------------------------------------------------------

------------------------------------------------------------------------

------------------------------------------------------------------------

For more information see the NWChem manual at

createfile: failed ga_create size=*********

------------------------------------------------------------------------

------------------------------------------------------------------------

 current input line :

    0:

------------------------------------------------------------------------

------------------------------------------------------------------------

------------------------------------------------------------------------

For more information see the NWChem manual at

http://www.emsl.pnl.gov/docs/nwchem/nwchem.html



------------------------------------------------------------------------

------------------------------------------------------------------------

 current input line :

    0:

------------------------------------------------------------------------

------------------------------------------------------------------------

------------------------------------------------------------------------

For more information see the NWChem manual at

http://www.emsl.pnl.gov/docs/nwchem/nwchem.html

 current input line :

    0:

------------------------------------------------------------------------

------------------------------------------------------------------------

------------------------------------------------------------------------

For more information see the NWChem manual at

http://www.emsl.pnl.gov/docs/nwchem/nwchem.html



------------------------------------------------------------------------

------------------------------------------------------------------------

For more information see the NWChem manual at

http://www.emsl.pnl.gov/docs/nwchem/nwchem.html




For further details see manual section:




7:7:createfile: failed ga_create size=:: 1662623641
    0:

------------------------------------------------------------------------

------------------------------------------------------------------------

------------------------------------------------------------------------

For more information see the NWChem manual at

http://www.emsl.pnl.gov/docs/nwchem/nwchem.html

------------------------------------------------------------------------

------------------------------------------------------------------------

 current input line : 

    0: 

------------------------------------------------------------------------

------------------------------------------------------------------------

http://www.emsl.pnl.gov/docs/nwchem/nwchem.html





For further details see manual section:
6:6:createfile: failed ga_create size=:: 1662623641


For further details see manual section:
3:3:createfile: failed ga_create size=:: 1662623641
(rank:3 hostname:c27.cluster.spms.ntu.edu.sg pid:17216):ARMCI DASSERT fail. armci.c:ARMCI_Error():260 cond:0




For further details see manual section:



(rank:7 hostname:c27.cluster.spms.ntu.edu.sg pid:17220):ARMCI DASSERT fail. armci.c:ARMCI_Error():260 cond:0


For further details see manual section:






------------------------------------------------------------------------

For more information see the NWChem manual at

http://www.emsl.pnl.gov/docs/nwchem/nwchem.html




For further details see manual section:




(rank:6 hostname:c27.cluster.spms.ntu.edu.sg pid:17219):ARMCI DASSERT fail. armci.c:ARMCI_Error():260 cond:0
4:4:createfile: failed ga_create size=:: 1662623641
(rank:4 hostname:c27.cluster.spms.ntu.edu.sg pid:17217):ARMCI DASSERT fail. armci.c
ARMCI_Error():260 cond:0
------------------------------------------------------------------------
5:5:createfile: failed ga_create size=:: 1662623641
(rank:5 hostname:c27.cluster.spms.ntu.edu.sg pid:17218):ARMCI DASSERT fail. armci.c
ARMCI_Error():260 cond:0
1:1:createfile: failed ga_create size=:: 1662623641
(rank:1 hostname:c27.cluster.spms.ntu.edu.sg pid:17214):ARMCI DASSERT fail. armci.c:ARMCI_Error():260 cond:0
2:2:createfile: failed ga_create size=:: 1662623641
(rank:2 hostname:c27.cluster.spms.ntu.edu.sg pid:17215):ARMCI DASSERT fail. armci.c:ARMCI_Error():260 cond:0
For more information see the NWChem manual at  http://www.emsl.pnl.gov/docs/nwchem/nwchem.html




For further details see manual section:




0:0:createfile: failed ga_create size=:: 1662623641
(rank:0 hostname:c27.cluster.spms.ntu.edu.sg pid:17213):ARMCI DASSERT fail. armci.c
ARMCI_Error():260 cond:0

The computation node I use has 8 processors and 62GB RAM.

What is going wrong there?


Forum >> NWChem's corner >> Running NWChem



Who's here now Members 0 Guests 0 Bots/Crawler 1

AWC's: 2.5.10 MediaWiki - Stand Alone Forum Extension
Forum theme style by: AWC
Retrieved from "http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id345/a_molpro_CCSD(t)_calculation_wit....html"