Energy calculation using CCSD

1

Hi,
My input file looks like this
memory 50GB
molecule dimer {
0 1
N -4.912476052773 -0.240906048411 -0.454102977275
C -3.558066814471 -0.468960834620 -0.352199435403
C -3.002370112563 0.805312698462 -0.179794526071
N -3.977513871134 1.789322746060 -0.175198888759
C -5.098258658319 1.124366688043 -0.340941710258
C -1.592759479874 0.863483346206 -0.046948759304
N -0.918397912501 -0.310149202713 -0.097741427891
C -1.591620699450 -1.467059749712 -0.269211453889
N -2.906429694590 -1.643752925003 -0.405368214674
H 0.110363162857 2.004505274361 0.205319340699
N -0.913812304897 2.008795681429 0.124196344025
H -5.622486929790 -0.950303919327 -0.586469281699
H -6.090999499579 1.568401075694 -0.389512121692
H -1.434724200397 2.874605694705 0.152741228754
H -0.955641163552 -2.358051919702 -0.296719887214
C 4.018105805762 0.579709545714 0.385699215928
C 4.544449463700 -0.668375484144 0.320109508135
N 3.761175140822 -1.789730625330 0.160794859099
C 2.371523272523 -1.746759412429 0.052025936964
N 1.851785242357 -0.470921056997 0.122656200879
C 2.560590188573 0.709171466581 0.281433783193
O 1.697343166563 -2.754409135170 -0.091296586218
C 4.823939331413 1.832467103084 0.556699474749
O 1.978044200947 1.799005004820 0.330229143049
H 5.618449846571 -0.852398626466 0.390192807241
H 4.169655481035 -2.715386973400 0.112146826484
H 0.798402993760 -0.401716522356 0.042371721525
H 5.900483012221 1.615992059111 0.625618906388
H 4.653733764299 2.521737631920 -0.286469438029
H 4.511650205357 2.374300651591 1.464317556683
units angstrom
}
set {
basis aug-cc-pVDZ
scf_type df
maxiter 500
step_type nr
}
energy(‘ccsd’)

and I received an error to contact developer, Please see the error ,

PSIO_ERROR: unit = 102, errval = 21
Traceback (most recent call last):
File “/storage/praha1/home/mmithun/miniconda3/bin/psi4”, line 338, in
exec(content)
File “”, line 59, in
File “/storage/praha1/home/mmithun/miniconda3/lib//python3.10/site-packages/psi4/driver/driver.py”, line 526, in energy
wfn = procedures[‘energy’][lowername](lowername, molecule=molecule, **kwargs)
File “/storage/praha1/home/mmithun/miniconda3/lib//python3.10/site-packages/psi4/driver/procrouting/proc.py”, line 868, in select_ccsd
return func(name, **kwargs)
File “/storage/praha1/home/mmithun/miniconda3/lib//python3.10/site-packages/psi4/driver/procrouting/proc.py”, line 2898, in run_ccenergy
core.cctransort(ref_wfn)

RuntimeError:
Fatal Error: PSIO_ERROR: 21 (File not opened)
You need to open file 102 before you attempt this operation,
If you’re a user, contact developers immediately. This is a bug.
If you’re a developer, get yourself some coffee.

Error occurred in file: /scratch/psilocaluser/conda-builds/psi4-multiout_1670993662927/work/psi4/src/psi4/libpsio/error.cc on line: 134
The most recent 5 function calls were:

psi::PSIO::wt_toclen(unsigned long, unsigned long)
psi::PSIO::write(unsigned long, char const*, char*, unsigned long, psi::psio_address, psi::psio_address*)

Printing out the relevant lines from the Psithon → Python processed input file:
core.IO.set_default_namespace(“dimer”)
core.set_global_option(“BASIS”, “aug-cc-pVDZ”)
core.set_global_option(“SCF_TYPE”, “df”)
core.set_global_option(“MAXITER”, 500)
core.set_global_option(“STEP_TYPE”, “nr”)
→ energy(‘ccsd’)

!----------------------------------------------------------------------------------!
! !
! Fatal Error: PSIO_ERROR: 21 (File not opened) !
! You need to open file 102 before you attempt this operation, !
! If you’re a user, contact developers immediately. This is a bug. !
! If you’re a developer, get yourself some coffee. !
! Error occurred in file: /scratch/psilocaluser/conda- !
! builds/psi4-multiout_1670993662927/work/psi4/src/psi4/libpsio/error.cc on !
! line: 134 !
! The most recent 5 function calls were: !
! psi::PSIO::wt_toclen(unsigned long, unsigned long) !
! psi::PSIO::write(unsigned long, char const*, char*, unsigned long, !
! psi::psio_address, psi::psio_address*) !
! !
!----------------------------------------------------------------------------------!

PLease let me know if I can modify my input file.

Thanks in advance.

2

Can you provide your output file so that we can get a better idea of where the calculation crashed?

3

sorry for delay. Please find the fresh files and error here.
error :

PSIO_ERROR: unit = 102, errval = 21
Traceback (most recent call last):
File “/storage/praha1/home/mmithun/miniconda3/bin/psi4”, line 338, in
exec(content)
File “”, line 59, in
File “/storage/praha1/home/mmithun/miniconda3/lib//python3.10/site-packages/psi4/driver/driver.py”, line 526, in energy
wfn = procedures[‘energy’][lowername](lowername, molecule=molecule, **kwargs)
File “/storage/praha1/home/mmithun/miniconda3/lib//python3.10/site-packages/psi4/driver/procrouting/proc.py”, line 868, in select_ccsd
return func(name, **kwargs)
File “/storage/praha1/home/mmithun/miniconda3/lib//python3.10/site-packages/psi4/driver/procrouting/proc.py”, line 2898, in run_ccenergy
core.cctransort(ref_wfn)

RuntimeError:
Fatal Error: PSIO_ERROR: 21 (File not opened)
You need to open file 102 before you attempt this operation,
If you’re a user, contact developers immediately. This is a bug.
If you’re a developer, get yourself some coffee.

Error occurred in file: /scratch/psilocaluser/conda-builds/psi4-multiout_1670993662927/work/psi4/src/psi4/libpsio/error.cc on line: 134
The most recent 5 function calls were:

psi::PSIO::wt_toclen(unsigned long, unsigned long)
psi::PSIO::write(unsigned long, char const*, char*, unsigned long, psi::psio_address, psi::psio_address*)

Printing out the relevant lines from the Psithon → Python processed input file:
core.IO.set_default_namespace(“dimer”)
core.set_global_option(“BASIS”, “aug-cc-pVDZ”)
core.set_global_option(“SCF_TYPE”, “df”)
core.set_global_option(“MAXITER”, 500)
core.set_global_option(“STEP_TYPE”, “nr”)
→ energy(‘ccsd’)

!----------------------------------------------------------------------------------!
! !
! Fatal Error: PSIO_ERROR: 21 (File not opened) !
! You need to open file 102 before you attempt this operation, !
! If you’re a user, contact developers immediately. This is a bug. !
! If you’re a developer, get yourself some coffee. !
! Error occurred in file: /scratch/psilocaluser/conda- !
! builds/psi4-multiout_1670993662927/work/psi4/src/psi4/libpsio/error.cc on !
! line: 134 !
! The most recent 5 function calls were: !
! psi::PSIO::wt_toclen(unsigned long, unsigned long) !
! psi::PSIO::write(unsigned long, char const*, char*, unsigned long, !
! psi::psio_address, psi::psio_address*) !
! !
!----------------------------------------------------------------------------------!

and the input and out are attached.
psi.txt (2.2 KB)
psi-out.txt (32.2 KB)

4

It’s not immediately clear what caused the problem, but I suspect you’re out of disk space? The four-virtual-index integrals alone require 384 GB of storage, and the three-virtual-index integrals need another 56 GB.

Some suggestions:

(1) Do not set scf_type df. The particular coupled cluster energy code you’re using in Psi4 only runs correctly with scf_type pk. (And we should identify such cases and trap the error.)

(2) You should definitely freeze the core orbitals because it will speed up the calculation and the basis set you’re using isn’t designed to correlate the core anyway. Set freeze_core true.

(3) I suggest you set cachelevel 0 to avoid memory fragmentation that can sometimes happen for larger calculations.