ECP use in optimize(ccsd(t))

conda remove v2rdm_casscf

Mac or Linux?

Is your FATAL error before, during, or after update?

Linux. Before update.

Ok. v2rdm is never required for operation. Whenever it gives trouble, just remove it.

This command is not very clear. Is this a single line or multiple lines?

I get the following when I do a test run:

…/lib/python3.5/site-packages/psi4/tests/test_aaa_profiling.py::test_threaded_blas
xfail
…/lib/python3.5/site-packages/psi4/tests/test_addons.py::test_gdma PASSED
…/lib/python3.5/site-packages/psi4/tests/test_addons.py::test_mrcc SKIPPED
…/lib/python3.5/site-packages/psi4/tests/test_addons.py::test_chemps2 PASSED
…/lib/python3.5/site-packages/psi4/tests/test_addons.py::test_dftd3 FAILED
…/lib/python3.5/site-packages/psi4/tests/test_addons.py::test_libefp PASSED
…/lib/python3.5/site-packages/psi4/tests/test_addons.py::test_pcmsolver PASSED
…/lib/python3.5/site-packages/psi4/tests/test_addons.py::test_erd PASSED
…/lib/python3.5/site-packages/psi4/tests/test_addons.py::test_simint PASSED
…/lib/python3.5/site-packages/psi4/tests/test_addons.py::test_json PASSED
…/lib/python3.5/site-packages/psi4/tests/test_addons.py::test_cfour PASSED
…/lib/python3.5/site-packages/psi4/tests/test_addons.py::test_v2rdm_casscf FAILED
…/lib/python3.5/site-packages/psi4/tests/test_addons.py::test_grimme_3c FAILED
…/lib/python3.5/site-packages/psi4/tests/test_psi4.py::test_psi4_basic PASSED
…/lib/python3.5/site-packages/psi4/tests/test_psi4.py::test_psi4_cas PASSED
…/lib/python3.5/site-packages/psi4/tests/test_psi4.py::test_psi4_cc PASSED
…/lib/python3.5/site-packages/psi4/tests/test_psi4.py::test_psi4_dfmp2 PASSED
…/lib/python3.5/site-packages/psi4/tests/test_psi4.py::test_psi4_sapt PASSED
…/lib/python3.5/site-packages/psi4/tests/test_psi4.py::test_psi4_scfproperty PASSED

the above should be conda update psi4 -c psi4/label/dev -c psi4 . single line

conda update dftd3 v2rdm_casscf gcp -c psi4/label/dev -c psi4 for the FAILEDs

packages in environment at /home/dash/psi4conda:

alabaster 0.7.10 py36_0
asn1crypto 0.22.0 py36_0
babel 2.5.0 py36_0
bzip2 1.0.6 3
certifi 2016.2.28 py36_0
cffi 1.10.0 py36_0
chemps2 1.8.3 5
cloog 0.18.0 0
cmake 3.6.3 0
conda 4.3.27 py36h2866c0b_0
conda-env 2.6.0 0
cryptography 1.8.1 py36_0
curl 7.52.1 0
dftd3 3.2.0 7
dkh 1.2 1 psi4/label/dev
erd 3.0.6 0
expat 2.1.0 0
gcc-5 5.2.0 1
gcc-5-mp 5.2.0 0
gcp 2.0.1 0
gdma 2.2.6 2
gmp 6.1.0 0
hdf5 1.8.17 1
idna 2.6 py36_0
imagesize 0.7.1 py36_0
isl 0.12.2 0
jinja2 2.9.6 py36_0
libefp 1.5b1 0 psi4/label/dev
libffi 3.2.1 1
libint 1.2.1 1 psi4/label/dev
libxc 3.0.0 6 psi4/label/dev
markupsafe 1.0 py36_0
mkl 2017.0.3 0
mpc 1.0.1 0
mpfr 3.1.2 0
ncurses 5.9 10
numpy 1.13.1 py36_0
openssl 1.0.2k 1
packaging 16.8 py36_0
pcmsolver 1.1.10 py36_1 psi4/label/dev
pip 9.0.1 py36_1
psi4 1.2a1.dev597+0ddc90a py36_0 psi4/label/dev
psi4-lt-mp 1.2a1.dev3 py36_0 psi4/label/dev
py 1.4.34 py36_0
pyasn1 0.2.3 py36_0
pycosat 0.6.2 py36_0
pycparser 2.18 py36_0
pygments 2.2.0 py36_0
pyopenssl 17.0.0 py36_0
pyparsing 2.2.0 py36_0
pytest 3.2.1 py36_0
python 3.6.2 0
pytz 2017.2 py36_0
readline 6.2 2
requests 2.14.2 py36_0
ruamel_yaml 0.11.14 py36_1
setuptools 36.4.0 py36_1
simint 0.7 0
six 1.10.0 py36_0
snowballstemmer 1.2.1 py36_0
sqlite 3.13.0 0
tk 8.5.18 0
v2rdm_casscf 0.4 py36_1 psi4/label/dev
wheel 0.29.0 py36_0
xz 5.2.2 1
yaml 0.1.6 0
zlib 1.2.8 3

Now I get this error:

File “/home/dash/psi4conda/lib//python3.6/site-packages/psi4/init.py”, line 55, in
from . import core
ImportError: /home/dash/psi4conda/lib//python3.6/site-packages/psi4/core.so: undefined symbol: __svml_sin4

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/home/dash/psi4conda/bin/psi4”, line 158, in
import psi4
File “/home/dash/psi4conda/lib//python3.6/site-packages/psi4/init.py”, line 60, in
raise ImportError("{0}".format(err))
ImportError: /home/dash/psi4conda/lib//python3.6/site-packages/psi4/core.so: undefined symbol: __svml_sin4

Looks like chemps2 didn’t get updated. For good measure, just conda update chemps2 dftd3 dkh erd gcp gdma libefp libint libxc simint v2rdm_casscf -c psi4/label/dev -c psi4
I’ll have to pin the buildno of chemps2, too, it looks like.

…/lib/python3.6/site-packages/psi4/tests/test_addons.py::test_gdma WARNING: string truncated
PASSED
…/lib/python3.6/site-packages/psi4/tests/test_addons.py::test_mrcc SKIPPED
…/lib/python3.6/site-packages/psi4/tests/test_addons.py::test_chemps2 PASSED
…/lib/python3.6/site-packages/psi4/tests/test_addons.py::test_dftd3 FAILED
…/lib/python3.6/site-packages/psi4/tests/test_addons.py::test_libefp LIBEFP: unable to open file /tmp/psi.10551…dftd3.2f9e5b94/h2o.efp
LIBEFP: unable to open file /h2o.efp
LIBEFP: unable to open file /tmp/psi.10551…dftd3.2f9e5b94/nh3.efp
LIBEFP: unable to open file /nh3.efp
PASSED
…/lib/python3.6/site-packages/psi4/tests/test_addons.py::test_pcmsolver PASSED
…/lib/python3.6/site-packages/psi4/tests/test_addons.py::test_erd PASSED
…/lib/python3.6/site-packages/psi4/tests/test_addons.py::test_simint PASSED
…/lib/python3.6/site-packages/psi4/tests/test_addons.py::test_json PASSED
…/lib/python3.6/site-packages/psi4/tests/test_addons.py::test_cfour PASSED
…/lib/python3.6/site-packages/psi4/tests/test_addons.py::test_v2rdm_casscf PASSED
…/lib/python3.6/site-packages/psi4/tests/test_addons.py::test_grimme_3c FAILED
…/lib/python3.6/site-packages/psi4/tests/test_addons.py::test_dkh PASSED
…/lib/python3.6/site-packages/psi4/tests/test_psi4.py::test_psi4_basic PASSED
…/lib/python3.6/site-packages/psi4/tests/test_psi4.py::test_psi4_cc PASSED
…/lib/python3.6/site-packages/psi4/tests/test_psi4.py::test_psi4_cas PASSED
…/lib/python3.6/site-packages/psi4/tests/test_psi4.py::test_psi4_dfmp2 PASSED
…/lib/python3.6/site-packages/psi4/tests/test_psi4.py::test_psi4_sapt PASSED
…/lib/python3.6/site-packages/psi4/tests/test_psi4.py::test_psi4_scfproperty PASSED
=========================================================== short test summary info ===========================================================
SKIP [1] lib/python3.6/site-packages/psi4/tests/test_addons.py:91: Psi4 not detecting MRCC. Add dmrcc to envvar PSIPATH or PATH

Conda list:

packages in environment at /home/dash/psi4conda:

alabaster 0.7.10 py36_0
asn1crypto 0.22.0 py36_0
babel 2.5.0 py36_0
bzip2 1.0.6 3
certifi 2016.2.28 py36_0
cffi 1.10.0 py36_0
chemps2 1.8.4 0 psi4/label/dev
cloog 0.18.0 0
cmake 3.6.3 0
conda 4.3.27 py36h2866c0b_0
conda-env 2.6.0 0
cryptography 1.8.1 py36_0
curl 7.52.1 0
dftd3 3.2.0 7
dkh 1.2 1 psi4/label/dev
erd 3.0.6 1 psi4/label/dev
expat 2.1.0 0
gcc-5 5.2.0 1
gcc-5-mp 5.2.0 0
gcp 2.0.1 0
gdma 2.2.6 3 psi4/label/dev
gmp 6.1.0 0
hdf5 1.8.17 1
idna 2.6 py36_0
imagesize 0.7.1 py36_0
isl 0.12.2 0
jinja2 2.9.6 py36_0
libefp 1.5b1 0 psi4/label/dev
libffi 3.2.1 1
libint 1.2.1 1 psi4/label/dev
libxc 3.0.0 6 psi4/label/dev
markupsafe 1.0 py36_0
mkl 2017.0.3 0
mpc 1.0.1 0
mpfr 3.1.2 0
ncurses 5.9 10
numpy 1.13.1 py36_0
openssl 1.0.2k 1
packaging 16.8 py36_0
pcmsolver 1.1.10 py36_1 psi4/label/dev
pip 9.0.1 py36_1
psi4 1.2a1.dev597+0ddc90a py36_0 psi4/label/dev
psi4-lt-mp 1.2a1.dev3 py36_0 psi4/label/dev
py 1.4.34 py36_0
pyasn1 0.2.3 py36_0
pycosat 0.6.2 py36_0
pycparser 2.18 py36_0
pygments 2.2.0 py36_0
pyopenssl 17.0.0 py36_0
pyparsing 2.2.0 py36_0
pytest 3.2.1 py36_0
python 3.6.2 0
pytz 2017.2 py36_0
readline 6.2 2
requests 2.14.2 py36_0
ruamel_yaml 0.11.14 py36_1
setuptools 36.4.0 py36_1
simint 0.7 0
six 1.10.0 py36_0
snowballstemmer 1.2.1 py36_0
sqlite 3.13.0 0
tk 8.5.18 0
v2rdm_casscf 0.4 py36_1 psi4/label/dev
wheel 0.29.0 py36_0
xz 5.2.2 1
yaml 0.1.6 0
zlib 1.2.8 3

Could you please send me your input file, my basis file as you have it and how you execute it? I sincerely appreciate your continued effort; unfortunately I don’t seem to be able to get the desired output.

Dear Lori,

Thank you very much for your help. I spoke too soon. There were some issues with my glibc; but now after taking into account your suggestions to update; the runs look fine.

Thanks a lot.

Best,
Monika

Dear Lori,

Now, the ECPs are read in. However, I have another issue. Upon optimizing the geometry; the C-C bonds change upto the order of 1.92 angstrom compared to a starting value of 1.45 angstrom (my expectation was that they would increase to a max of 1.47 angstrom). Also the C=C bond goes upto 1.83 angstrom from 1.34 angstrom. The displacements are huge? How do I prevent this?

There could be a problem with ECP optimizations, but plain optimization is the first culprit to examine. I’d do a plain b3lyp optimization (without ECPs), use that opt geom to seed a b3lyp opt with ECPs, and then use that opt to seed the calc you want. That should help clarify who (optimizer, ecp tech, ccsd(t)) is going amiss.

Already with the plain b3lyp optimization without ECPs, I start getting wierd geometries.
1 R(1,2) = 1.631807 -1.366196 0.000090 1.631898
2 R(1,3) = 1.607499 -1.618463 -0.002252 1.605247
3 R(1,7) = 0.189626 257.348291 0.356688 0.546314
4 R(2,4) = 1.607499 -1.618463 -0.002252 1.605247
Here R(1,2) is the C-C bond and R(1,3)=R(2,4) is the C=C bond.

You can try some of these.

No improvement. I tried setting the dynamic_level to 1 and opt_coordinates to both; but still the same issue.

this ok?

in:

psi4.core.clean()
psi4.set_memory('2 GB')
buta = psi4.geometry("""
units bohr
C -1.1579352682 -0.7336520997 0.0000000000
C 1.1579352682 0.7336520997 0.0000000000
C -3.4664188656 0.2981874225 0.0000000000
C 3.4664188656 -0.2981874225 0.0000000000
H -3.7066332742 2.3264227662 0.0000000000
H 3.7066332742 -2.3264227662 0.0000000000
H -0.9631933359 -2.7721807808 0.0000000000
H 0.9631933359 2.7721807808 0.0000000000
H -5.1469502967 -0.8555507642 0.0000000000
H 5.1469502967 0.8555507642 0.0000000000
""")

# E = psi4.energy('hf/monika')
# print(E)

psi4.set_options({
#'scf_type': 'cd',
'cc_type': 'cd',
#'basis': 'monika',
'basis': 'cc-pvdz',
'freeze_core': 'true'})

# E = psi4.energy('ccsd(t)')
# print(E)  # -26.685125334
#E = psi4.optimize('ccsd(t)')
E = psi4.optimize('b3lyp')
print(E)

out:

  ==> Optimization Summary <==

  Measures of convergence in internal coordinates in au.
  --------------------------------------------------------------------------------------------------------------- ~
   Step         Total Energy             Delta E       MAX Force       RMS Force        MAX Disp        RMS Disp  ~
  --------------------------------------------------------------------------------------------------------------- ~
      1    -155.999976741821   -155.999976741821      0.00948087      0.00458003      0.02609437      0.01254086  ~
      2    -156.000849275315     -0.000872533494      0.00207205      0.00055876      0.00332582      0.00119130  ~
      3    -156.000860380079     -0.000011104764      0.00017256      0.00007484      0.00132742      0.00047736  ~
      4    -156.000861080636     -0.000000700556      0.00003351      0.00001186      0.00027289      0.00008751  ~
  --------------------------------------------------------------------------------------------------------------- ~

	Writing optimization data to binary file.
	Final energy is   -156.0008610806356
	Final (previous) structure:
	Cartesian Geometry (in Angstrom)
	    C    -0.6199718128  -0.3840169566   0.0000000000
	    C     0.6199718128   0.3840169566   0.0000000000
	    C    -1.8478084960   0.1601039303   0.0000000000
	    C     1.8478084960  -0.1601039303   0.0000000000
	    H    -1.9885904468   1.2454045686   0.0000000000
	    H     1.9885904468  -1.2454045686   0.0000000000
	    H    -0.5150266183  -1.4757986622   0.0000000000
	    H     0.5150266183   1.4757986622   0.0000000000
	    H    -2.7475823205  -0.4587308968   0.0000000000
	    H     2.7475823205   0.4587308968   0.0000000000