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You can choose an avatar and change the default style by going to "Profile" → "Personality" or "Display".#1 2023-04-27 16:17:36
- Okko
- Member
- Registered: 2023-04-27
- Posts: 11
Calculation of Gibb's free energies and convergence problems
Dear all,
I am interested in calculating the Gibb's free energy of certain molecules at elevated temperatures. I started with smaller systems, e.g., O2 or H2O which finished successfully. However, for bigger system I encounter either 1) "convergence problem" at the end of the run or even before finishing the calculation immediately after the 2) "numerical differentiation". The geometries of all structures have been optimized yielding stationary points at the same level of theory as well as basis set and subsequently used for the Gibb's free energy calculation.
Used input file:
>> export MOLCAS_PRINT=verbose
>> export MOLCAS_MOLDEN=ON
>> export OMP_NUM_THREADS=1
>> export MOLCAS_MEM = 12500
&GATEWAY
Title= PoOH
Coord= $CurrDir/PoOH.Opt.xyz
Basis set
ANO-RCC-VTZP
Group= NoSym
Symt = 0.0
>> Do While
&SEWARD
cholesky
End of input
&SCF
End of input
&MBPT2
End of input
&SLAPAF &End
Numerical Hessian
THERmochemistry = 1
1.0
773.15 ; 783.15 ; 793.15 ; 803.15 ; 813.15 ; 823.15 ; 833.15 ; 843.15 ; 853.15 ; 863.15 ; 873.15; End of PT
End of input
>> EndDo
&MCKINLEY
End of inputObtained interesting part of the output file after finishing the numerical differentation for the first case 1):
Accumulate the gradient for selected numerical differentiation.
42 of 43
New Cartesian coordinates were found in 3 Newton-Raphson iterations.
**********************************************************************************************************************
* Energy Statistics for Geometry Optimization *
**********************************************************************************************************************
Energy Grad Grad Step Estimated Geom Hessian
Iter Energy Change Norm Max Element Max Element Final Energy Update Update Index
1 -22474.70845994 0.00000000 0.115981 0.063441 nrc005 0.010000 nrc001 -22474.70845994 NumHss None -99
2 -22474.70845002 0.00000992 0.086893 0.048712 nrc005 -0.020000 nrc001 -22474.70845002 NumHss None -99
3 -22474.70844954 0.00000048 0.116034 0.063350 nrc005 0.010000 nrc001 -22474.70844954 NumHss None -99
4 -22474.70872318 -0.00027364 0.114168 0.063124 nrc005 -0.020000 nrc002 -22474.70872318 NumHss None -99
5 -22474.70817672 0.00054647 0.120120 0.065382 nrc005 0.010000 nrc002 -22474.70817672 NumHss None -99
6 -22474.70739499 0.00078173 0.184191 0.227682 nrc014 -0.020000 nrc003 -22474.70739499 NumHss None -99
7 -22474.70828005 -0.00088506 0.120511 0.065968 nrc005 0.010000 nrc003 -22474.70828005 NumHss None -99
8 -22474.70827597 0.00000408 0.119180 0.064257 nrc005 -0.020000 nrc004 -22474.70827597 NumHss None -99
9 -22474.70858073 -0.00030476 0.084753 0.046681 nrc005 0.010000 nrc004 -22474.70858073 NumHss None -99
10 -22474.70907475 -0.00049402 0.110160 0.058846 nrc005 -0.020000 nrc005 -22474.70907475 NumHss None -99
11 -22474.70779056 0.00128419 0.093831 0.053997 nrc005 0.010000 nrc005 -22474.70779056 NumHss None -99
12 -22474.70848635 -0.00069578 0.116523 0.064044 nrc005 -0.020000 nrc006 -22474.70848635 NumHss None -99
13 -22474.70839396 0.00009238 0.116508 0.063545 nrc005 0.010000 nrc006 -22474.70839396 NumHss None -99
14 -22474.70811944 0.00027453 0.119590 0.064305 nrc005 -0.020000 nrc007 -22474.70811944 NumHss None -99
15 -22474.70876388 -0.00064445 0.114551 0.064164 nrc005 0.010000 nrc007 -22474.70876388 NumHss None -99
16 -22474.70840035 0.00036353 0.084446 0.047666 nrc005 -0.020000 nrc008 -22474.70840035 NumHss None -99
17 -22474.70850356 -0.00010321 0.116826 0.063782 nrc005 0.010000 nrc008 -22474.70850356 NumHss None -99
18 -22474.70852684 -0.00002328 0.116534 0.063624 nrc005 -0.020000 nrc009 -22474.70852684 NumHss None -99
19 -22474.70837626 0.00015059 0.117737 0.064871 nrc005 0.010000 nrc009 -22474.70837626 NumHss None -99
20 -22474.70848307 -0.00010682 0.115267 0.063043 nrc005 -0.020000 nrc010 -22474.70848307 NumHss None -99
21 -22474.70842377 0.00005931 0.117630 0.064651 nrc005 0.010000 nrc010 -22474.70842377 NumHss None -99
22 -22474.70864703 -0.00022326 0.115950 0.063503 nrc005 -0.020000 nrc011 -22474.70864703 NumHss None -99
23 -22474.70825412 0.00039291 0.118334 0.065012 nrc005 0.010000 nrc011 -22474.70825412 NumHss None -99
24 -22474.70870250 -0.00044838 0.116505 0.064089 nrc005 -0.020000 nrc012 -22474.70870250 NumHss None -99
25 -22474.70819371 0.00050879 0.117469 0.064370 nrc005 0.010000 nrc012 -22474.70819371 NumHss None -99
26 -22474.70846800 -0.00027429 0.116541 0.063717 nrc005 -0.020000 nrc013 -22474.70846800 NumHss None -99
27 -22474.70844344 0.00002456 0.086264 0.048343 nrc005 0.010000 nrc013 -22474.70844344 NumHss None -99
28 -22474.70850923 -0.00006579 0.117026 0.064101 nrc005 -0.020000 nrc014 -22474.70850923 NumHss None -99
29 -22474.70839852 0.00011071 0.085987 0.048181 nrc005 0.010000 nrc014 -22474.70839852 NumHss None -99
30 -22474.70838050 0.00001802 0.117086 0.064101 nrc005 -0.020000 nrc015 -22474.70838050 NumHss None -99
31 -22474.70853232 -0.00015182 0.117158 0.064425 nrc005 0.010000 nrc015 -22474.70853232 NumHss None -99
32 -22474.70851770 0.00001462 0.116946 0.064159 nrc005 -0.020000 nrc016 -22474.70851770 NumHss None -99
33 -22474.70838215 0.00013555 0.117401 0.064387 nrc005 0.010000 nrc016 -22474.70838215 NumHss None -99
34 -22474.70867632 -0.00029417 0.115761 0.063306 nrc005 -0.020000 nrc017 -22474.70867632 NumHss None -99
35 -22474.70822825 0.00044807 0.117362 0.064388 nrc005 0.010000 nrc017 -22474.70822825 NumHss None -99
36 -22474.70843462 -0.00020638 0.117160 0.064285 nrc005 -0.020000 nrc018 -22474.70843462 NumHss None -99
37 -22474.70848410 -0.00004948 0.117119 0.064225 nrc005 0.010000 nrc018 -22474.70848410 NumHss None -99
38 -22474.70849182 -0.00000771 0.117087 0.064254 nrc005 -0.020000 nrc019 -22474.70849182 NumHss None -99
39 -22474.70842672 0.00006510 0.117238 0.064278 nrc005 0.010000 nrc019 -22474.70842672 NumHss None -99
40 -22474.70847993 -0.00005322 0.117097 0.064248 nrc005 -0.020000 nrc020 -22474.70847993 NumHss None -99
41 -22474.70843846 0.00004147 0.117099 0.064228 nrc005 0.010000 nrc020 -22474.70843846 NumHss None -99
42 -22474.70844261 -0.00000414 0.116001 0.063446 nrc005 -0.020000 nrc021 -22474.70844261 NumHss None -99
++ Geometry section
********************************************************************************
Geometrical information of the new structure
********************************************************************************
*********************************************************
* Nuclear coordinates for the next iteration / Bohr *
*********************************************************
ATOM X Y Z
PO1 0.009603 -0.054941 0.462822
O2 0.043318 3.770800 -0.353947
O3 -0.153290 -3.904908 -0.358894
O4 -3.031749 -0.125963 -1.760649
O5 3.085356 0.137998 -1.749282
H6 1.335023 4.231547 -1.664825
H7 -1.404077 -4.244661 -1.546274
H8 -3.246819 1.692893 -2.185126
H9 3.362635 -1.502766 -2.239886
*********************************************************
* Nuclear coordinates for the next iteration / Angstrom *
*********************************************************
ATOM X Y Z
PO1 0.005081 -0.029073 0.244915
O2 0.022923 1.995422 -0.187301
O3 -0.081118 -2.066388 -0.189918
O4 -1.604333 -0.066657 -0.931695
O5 1.632700 0.073025 -0.925680
H6 0.706464 2.239238 -0.880987
H7 -0.743006 -2.246178 -0.818253
H8 -1.718142 0.895840 -1.156319
H9 1.779430 -0.795230 -1.185297which gives the Gibb's free energies in the requested temperature range but with a convergence problem at the end of the run
and again more or less the same problem, i.e., the second case 2) for a different (bigger) system demanding more than 50 numerical differentation steps:
Accumulate the gradient for selected numerical differentiation.
50 of 67
New Cartesian coordinates were found in 3 Newton-Raphson iterations.
**********************************************************************************************************************
* Energy Statistics for Geometry Optimization *
**********************************************************************************************************************
Energy Grad Grad Step Estimated Geom Hessian
Iter Energy Change Norm Max Element Max Element Final Energy Update Update Index
1 -7244.50408193 0.00000000 0.002117 0.001414 nrc025 0.010000 nrc001 -7244.50408193 NumHss None -99
2 -7244.50407224 0.00000969 0.004104 -0.001873 nrc001 -0.020000 nrc001 -7244.50407224 NumHss None -99
3 -7244.50407253 -0.00000029 0.004883 0.001900 nrc001 0.010000 nrc001 -7244.50407253 NumHss None -99
4 -7244.50407045 0.00000208 0.005643 -0.003072 nrc024 -0.020000 nrc002 -7244.50407045 NumHss None -99
5 -7244.50407045 0.00000001 0.005682 0.002472 nrc002 0.010000 nrc002 -7244.50407045 NumHss None -99
6 -7244.50407194 -0.00000150 0.004669 -0.001797 nrc003 -0.020000 nrc003 -7244.50407194 NumHss None -99
7 -7244.50407194 0.00000001 0.004709 0.001867 nrc003 0.010000 nrc003 -7244.50407194 NumHss None -99
8 -7244.50405796 0.00001398 0.006780 -0.004475 nrc004 -0.020000 nrc004 -7244.50405796 NumHss None -99
9 -7244.50401887 0.00003909 0.008074 0.005274 nrc004 0.010000 nrc004 -7244.50401887 NumHss None -99
10 -7244.50401884 0.00000002 0.005961 0.004438 nrc025 -0.020000 nrc005 -7244.50401884 NumHss None -99
11 -7244.50405602 -0.00003718 0.006690 0.004199 nrc005 0.010000 nrc005 -7244.50405602 NumHss None -99
12 -7244.50405824 -0.00000222 0.004774 -0.002949 nrc006 -0.020000 nrc006 -7244.50405824 NumHss None -99
13 -7244.50405821 0.00000003 0.004801 0.002963 nrc006 0.010000 nrc006 -7244.50405821 NumHss None -99
14 -7244.50404104 0.00001717 0.007993 -0.004243 nrc007 -0.020000 nrc007 -7244.50404104 NumHss None -99
15 -7244.50404103 0.00000001 0.008103 0.004082 nrc007 0.010000 nrc007 -7244.50404103 NumHss None -99
16 -7244.50405508 -0.00001405 0.005285 -0.003588 nrc008 -0.020000 nrc008 -7244.50405508 NumHss None -99
17 -7244.50402915 0.00002593 0.008982 0.006011 nrc008 0.010000 nrc008 -7244.50402915 NumHss None -99
18 -7244.50405767 -0.00002852 0.005395 -0.002934 nrc009 -0.020000 nrc009 -7244.50405767 NumHss None -99
19 -7244.50405779 -0.00000012 0.006199 0.003640 nrc009 0.010000 nrc009 -7244.50405779 NumHss None -99
20 -7244.50405416 0.00000363 0.005730 0.003480 nrc020 -0.020000 nrc010 -7244.50405416 NumHss None -99
21 -7244.50405416 -0.00000000 0.005758 0.004025 nrc024 0.010000 nrc010 -7244.50405416 NumHss None -99
22 -7244.50406888 -0.00001472 0.003405 -0.002020 nrc011 -0.020000 nrc011 -7244.50406888 NumHss None -99
23 -7244.50407137 -0.00000249 0.004054 -0.002502 nrc022 0.010000 nrc011 -7244.50407137 NumHss None -99
24 -7244.50405265 0.00001873 0.004763 0.004329 nrc025 -0.020000 nrc012 -7244.50405265 NumHss None -99
25 -7244.50407074 -0.00001810 0.004067 0.002370 nrc008 0.010000 nrc012 -7244.50407074 NumHss None -99
26 -7244.50407416 -0.00000342 0.003168 -0.001257 nrc013 -0.020000 nrc013 -7244.50407416 NumHss None -99
27 -7244.50407417 -0.00000001 0.002793 0.001396 nrc013 0.010000 nrc013 -7244.50407417 NumHss None -99
28 -7244.50405809 0.00001608 0.004141 -0.002222 nrc022 -0.020000 nrc014 -7244.50405809 NumHss None -99
29 -7244.50407722 -0.00001914 0.001847 0.000849 nrc014 0.010000 nrc014 -7244.50407722 NumHss None -99
30 -7244.50407729 -0.00000007 0.001789 0.000890 nrc008 -0.020000 nrc015 -7244.50407729 NumHss None -99
31 -7244.50407972 -0.00000243 0.003171 -0.002062 nrc022 0.010000 nrc015 -7244.50407972 NumHss None -99
32 -7244.50405701 0.00002271 0.005953 -0.003416 nrc016 -0.020000 nrc016 -7244.50405701 NumHss None -99
33 -7244.50405701 0.00000000 0.006152 0.003364 nrc016 0.010000 nrc016 -7244.50405701 NumHss None -99
34 -7244.50407648 -0.00001947 0.003870 -0.001865 nrc017 -0.020000 nrc017 -7244.50407648 NumHss None -99
35 -7244.50407648 0.00000000 0.003619 0.002227 nrc020 0.010000 nrc017 -7244.50407648 NumHss None -99
36 -7244.50407832 -0.00000184 0.001816 0.000777 nrc008 -0.020000 nrc018 -7244.50407832 NumHss None -99
37 -7244.50405858 0.00001974 0.004530 0.003071 nrc025 0.010000 nrc018 -7244.50405858 NumHss None -99
38 -7244.50407217 -0.00001360 0.001404 -0.001222 nrc019 -0.020000 nrc019 -7244.50407217 NumHss None -99
39 -7244.50406014 0.00001204 0.004010 0.003629 nrc025 0.010000 nrc019 -7244.50406014 NumHss None -99
40 -7244.50405534 0.00000479 0.005947 0.004510 nrc024 -0.020000 nrc020 -7244.50405534 NumHss None -99
41 -7244.50405533 0.00000001 0.006210 -0.004914 nrc024 0.010000 nrc020 -7244.50405533 NumHss None -99
42 -7244.50406901 -0.00001368 0.002564 -0.002252 nrc021 -0.020000 nrc021 -7244.50406901 NumHss None -99
43 -7244.50406845 0.00000056 0.004635 0.003207 nrc021 0.010000 nrc021 -7244.50406845 NumHss None -99
44 -7244.50405238 0.00001607 0.005074 -0.006226 nrc022 -0.020000 nrc022 -7244.50405238 NumHss None -99
45 -7244.50406716 -0.00001478 0.002025 0.002318 nrc022 0.010000 nrc022 -7244.50406716 NumHss None -99
46 -7244.50405531 0.00001185 0.004899 0.003078 nrc024 -0.020000 nrc023 -7244.50405531 NumHss None -99
47 -7244.50405531 0.00000000 0.004825 0.003008 nrc020 0.010000 nrc023 -7244.50405531 NumHss None -99
48 -7244.50407246 -0.00001715 0.005290 -0.003465 nrc026 -0.020000 nrc024 -7244.50407246 NumHss None -99
49 -7244.50407246 -0.00000000 0.005089 0.003209 nrc026 0.010000 nrc024 -7244.50407246 NumHss None -99
50 -7244.50407501 -0.00000255 0.003908 0.002401 nrc008 -0.020000 nrc025 -7244.50407501 NumHss None -99
++ Geometry section
********************************************************************************
Geometrical information of the new structure
********************************************************************************
*********************************************************
* Nuclear coordinates for the next iteration / Bohr *
*********************************************************
ATOM X Y Z
TE1 -0.000000 -0.000001 -0.056443
O2 -2.683797 -0.252259 -2.540665
O3 2.683798 0.252268 -2.540662
O4 2.418943 -0.072459 2.590421
O5 -2.418946 0.072446 2.590419
O6 0.148577 -3.613763 -0.322990
O7 -0.148577 3.613762 -0.322974
H8 -2.954901 1.417916 -3.230516
H9 2.954904 -1.417904 -3.230519
H10 4.070367 -0.079590 1.806797
H11 -4.070369 0.079579 1.806793
H12 -1.278757 -4.139598 -1.338370
H13 1.278757 4.139601 -1.338349
*********************************************************
* Nuclear coordinates for the next iteration / Angstrom *
*********************************************************
ATOM X Y Z
TE1 -0.000000 -0.000001 -0.029868
O2 -1.420204 -0.133490 -1.344462
O3 1.420205 0.133495 -1.344460
O4 1.280050 -0.038344 1.370792
O5 -1.280051 0.038337 1.370791
O6 0.078624 -1.912321 -0.170919
O7 -0.078624 1.912321 -0.170910
H8 -1.563666 0.750329 -1.709515
H9 1.563668 -0.750322 -1.709517
H10 2.153945 -0.042117 0.956116
H11 -2.153946 0.042112 0.956114
H12 -0.676689 -2.190581 -0.708235
H13 0.676689 2.190583 -0.708224without giving any Gibb's free energy and stopping the calculation immediately due to a convergence problem.
My question is whether the used input file is correct or which additional parameters are required in the input file to overcome this convergence problem? Any suggestions?
If you need further information please let me know.
I am grateful for any hint!
Thanks in advance,
Okko
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#2 2023-04-28 13:09:21
- Ignacio
- Administrator
- From: Uppsala
- Registered: 2015-11-03
- Posts: 1,085
Re: Calculation of Gibb's free energies and convergence problems
For the second case, I guess you're hitting the default MOLCAS_MAXITER, which is 50. Change it with:
> EXPORT MOLCAS_MAXITER=200In any case, if you have optimized structures, I think you can simply run:
&GATEWAY
...
&SEWARD
...
&SCF
...
&MCKINLEY
...Offline
#3 2023-04-28 15:07:29
- Okko
- Member
- Registered: 2023-04-27
- Posts: 11
Re: Calculation of Gibb's free energies and convergence problems
Thank you for your suggestions, Ignacio! Just to clarify the last point. Since the structures are already optimized I can simply move the &MCKINLEY flag into the do-while loop and modify the input file accordingly, right?
>> export MOLCAS_PRINT=verbose
>> export MOLCAS_MOLDEN=ON
>> export OMP_NUM_THREADS=1
>> export MOLCAS_MAXITER=200
>> export MOLCAS_MEM=12500
&GATEWAY
Title= PoOH
Coord= $CurrDir/PoOH.Opt.xyz
Basis set
ANO-RCC-VTZP
Group= NoSym
Symt = 0.0
>> Do While
&SEWARD
cholesky
End of input
&SCF
End of input
&MBPT2
End of input
&MCKINLEY
End of input
&SLAPAF &End
Numerical Hessian
THERmochemistry = 1
1.0
773.15 ; 783.15 ; 793.15 ; 803.15 ; 813.15 ; 823.15 ; 833.15 ; 843.15 ; 853.15 ; 863.15 ; 873.15; End of PT
End of input
>> EndDoOffline
#4 2023-04-28 15:35:55
- Ignacio
- Administrator
- From: Uppsala
- Registered: 2015-11-03
- Posts: 1,085
Re: Calculation of Gibb's free energies and convergence problems
No, I mean that you don't need any loop or SLAPAF.
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#5 2023-05-23 13:09:57
- Okko
- Member
- Registered: 2023-04-27
- Posts: 11
Re: Calculation of Gibb's free energies and convergence problems
Great, thank you Ignacio! Last question related to the MCKINLEY module. As far as I understood the MCKINLEY module calls the SLAPAF module internally. Hence, I would like to know whether it is possible to investigate the temperature effect in terms of the Gibb's free energy for single atoms? I know that such calculations are doable employing other quantum-chemistry packages but when I try to run the calculation in OpenMolcas it leads to the following error "Too few atoms to relax". It's not surprising, since the ZPE contribution is equal to zero and therefore the numerical differentiation (when trying to displace the single atom) fails/stops at this stage.
I tried a quick fix by editing the source codes "slapaf_util/box.f, l 27ff" as well as "slapaf_util/bmtrx_internal.f, 161ff" but these edits resulted in new errors as expected. Is there an alternative solution or is it necessary to rewrite the corresponding source codes to calculate the Gibb's free energy of a single atom?
Thanks in advance!
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