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Pages: 1

#1 2018-07-29 10:13:41

wangjun
Member
Registered: 2015-12-09
Posts: 26

Is it possible to run dynamics for the system including isotope?

Dear molcas  experts,

I want to run dynamics simulations for the system including isotope ? Is is possible?
How to specify the isotope in the input?

Thanks in advance!

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#2 2018-07-30 08:36:22

Ignacio
Administrator
From: Uppsala
Registered: 2015-11-03
Posts: 1,085

Re: Is it possible to run dynamics for the system including isotope?

It's undocumented, but the code says:

C     The isotope keyword allows to change the mass of any atom
C
C     to change the mass of atom 3 to 5.0 Da and atom 4 to 9.0 Da:
C
C     ISOTOPE
C      2          * nIsotope
C      3 5.0      * isoatom(1)
C      4 9.0      * isoatom(2)

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#3 2018-07-30 19:07:13

wangjun
Member
Registered: 2015-12-09
Posts: 26

Re: Is it possible to run dynamics for the system including isotope?

thanks a lot, ignacio.

as you mentioned,
---------------------------------
ISOTOPE
    2          * nIsotope
    3 5.0      * isoatom(1)
    4 9.0      * isoatom(2)
---------------------------------
2,3,4 denotes the atom label in the xyz coordinate?
5.0 and 9.0 is the mass which I want to change ?
what does it mean, * nIsotope and * isoatom(1) ?

could you give me an example input of changing H20 (water) to D2O?

Thanks a lot!

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#4 2018-07-30 20:00:18

Ignacio
Administrator
From: Uppsala
Registered: 2015-11-03
Posts: 1,085

Re: Is it possible to run dynamics for the system including isotope?

2 is the number of isotope changes specified below. The other numbers should be clear from the sentence "to change the mass of atom 3 to 5.0 Da and atom 4 to 9.0 Da". In the molcas input, everything following a "*" until the end of the line is just a comment and is ignored.

If your water molecule is given as O, H, H,  you would change it to D2O with:

ISOTOPE
2
2 2.014
3 2.014

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#5 2018-07-31 07:54:14

wangjun
Member
Registered: 2015-12-09
Posts: 26

Re: Is it possible to run dynamics for the system including isotope?

thanks a lot

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#6 2018-07-31 08:10:07

wangjun
Member
Registered: 2015-12-09
Posts: 26

Re: Is it possible to run dynamics for the system including isotope?

when I try to use ISOTOPE keyword in the input, it does not work,

error information is
'ISOTOPE is not a keyword!, Error in keyword.'

my input is

&GATEWAY
  COORD = stru.xyz
  BASIS=  svp
  GROUP=  nosym
  RICD
  ISOTOPE
  2
  2 2.014
  3 2.014

>>  FOREACH  ITER  in  (1  ..  800)

&SEWARD
DoAnalytical

>>  IF  (  $ITER  =  1  )

&RASSCF
  LUMORB
  FileOrb=  $Project.GssOrb
  Symmetry= 1
  Spin=  1
  nActEl=  10  0  0
  Inactive=  0
  RAS2=  10
  CIroot=  2  2  1

>>  COPY  $Project.JobIph  $Project.JobOld

>>  ENDIF

&RASSCF
  JOBIPH;  CIRESTART
  Symmetry= 1
  Spin=  1
  nActEl=  10  0  0
  Inactive=  0
  RAS2=  10
  CIroot=  2  2  1
  MDRLXR=  2

>>  COPY  $Project.JobIph  $Project.JobOld

&ALASKA

#>> COPY $CurrDir/$Project.velocity.xyz .

&DYNAMIX
  VELVer
  DT=  40.0
  VELO=  0
  THER=  1
  HOP=   1

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#7 2018-07-31 10:35:42

Ignacio
Administrator
From: Uppsala
Registered: 2015-11-03
Posts: 1,085

Re: Is it possible to run dynamics for the system including isotope?

It is a DYNAMIX keyword, not GATEWAY.

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#8 2018-07-31 16:19:49

wangjun
Member
Registered: 2015-12-09
Posts: 26

Re: Is it possible to run dynamics for the system including isotope?

thanks for your reply. It does not work,

input

&GATEWAY
  COORD = stru.xyz
  BASIS=  svp
  GROUP=  nosym
  RICD


>>  FOREACH  ITER  in  (1  ..  800)

&SEWARD
DoAnalytical

>>  IF  (  $ITER  =  1  )

&RASSCF
  LUMORB
  FileOrb=  $Project.GssOrb
  Symmetry= 1
  Spin=  1
  nActEl=  10  0  0
  Inactive=  0
  RAS2=  10
  CIroot=  2  2  1

>>  COPY  $Project.JobIph  $Project.JobOld

>>  ENDIF

&RASSCF
  JOBIPH;  CIRESTART
  Symmetry= 1
  Spin=  1
  nActEl=  10  0  0
  Inactive=  0
  RAS2=  10
  CIroot=  2  2  1
  MDRLXR=  2

>>  COPY  $Project.JobIph  $Project.JobOld

&ALASKA


&DYNAMIX
  VELVer
  DT=  40.0
  VELO=  0
  THER=  1
  HOP=   1
  ISOTOPE
  2
  2 2.014
  3 2.014

>>  END  DO

and the error information is 

)()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
                                 MOLCAS executing module DYNAMIX with 15000 MB of memory
                                              at 17:17:53 Tue Jul 31 2018
()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()


0:Segmentation Violation error, status=: 11
(rank:0 hostname:n927 pid:23266):ARMCI DASSERT fail. src/common/signaltrap.c:SigSegvHandler():310 cond:0
--- Stop Module:  dynamix at Tue Jul 31 17:17:53 2018 /rc=                    -1 (Unknown) ---
 Aborting..
"dyn.log" 1367L, 61416C

if I remove the isotope lines, it works well.

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#9 2018-08-13 16:44:57

Ignacio
Administrator
From: Uppsala
Registered: 2015-11-03
Posts: 1,085

Re: Is it possible to run dynamics for the system including isotope?

It works for me. Which version are you using?

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#10 2018-08-19 17:09:21

wangjun
Member
Registered: 2015-12-09
Posts: 26

Re: Is it possible to run dynamics for the system including isotope?

I am using Molcas 8.0.

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#11 2018-08-21 11:19:45

wangjun
Member
Registered: 2015-12-09
Posts: 26

Re: Is it possible to run dynamics for the system including isotope?

which version are you using?

Ignacio wrote:

It works for me. Which version are you using?

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#12 2018-08-21 12:23:40

Ignacio
Administrator
From: Uppsala
Registered: 2015-11-03
Posts: 1,085

Re: Is it possible to run dynamics for the system including isotope?

Latest OpenMolcas. It's quite possible it doesn't work with Molcas 8.0

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#13 2018-08-22 10:34:19

wangjun
Member
Registered: 2015-12-09
Posts: 26

Re: Is it possible to run dynamics for the system including isotope?

Thanks a lot for your reply, Ignacio. Does the latest version of OpenMolcas include the module which can run surface hop semi-classical
molecular dynamics simualtion using Tully's fewest switches, along with the Hammes-Schiffer/Tully scheme and the decoherence correction
proposed by Granucci and Persico ? What are the main advantages of OpenMolcas comparing with professional version of Molcas?

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#14 2018-08-22 12:06:59

Ignacio
Administrator
From: Uppsala
Registered: 2015-11-03
Posts: 1,085

Re: Is it possible to run dynamics for the system including isotope?

Yes, it includes the surfacehop module. The main advantage is that it is open source and you can always get the latest development version.

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#15 2018-08-22 15:41:08

wangjun
Member
Registered: 2015-12-09
Posts: 26

Re: Is it possible to run dynamics for the system including isotope?

Great! Thank you very much, Ignacio.

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