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Pages: 1

#1 2022-11-01 02:25:40

zz
Member
Registered: 2022-10-17
Posts: 13

Loop failure

I am using the foreach command to try to do calculation with different structures but the output file shows that the loop is always the same, and the coordinates are always the ones entered in the first loop

 >>export dist=1.7035463
 >>export bond=1.7109785
 >>>FOREACH L in (0,1,2,3,4,5,6,7,8,9,10)
 >>eval dist=$dist+$L/100
 >>eval bond=$bond+$L/100
  &GATEWAY 
    TITLE
    UO2-DGA
    Symmetry
    X
    XBAS
    U.ANO-RCC-VTZP 
    O.ANO-RCC-VDZP 
    N.ANO-RCC-VDZ
    H.ANO-RCC-VDZ
    C.ANO-RCC-VDZ
    end of basis
    ZMAT
    U1      
    O2 1 $dist   
    X3 1 1.9531593 2 90  
    O4 1 2.7221484 2 92.8078917 3 90
    O5 1 $bond 2 178.9268708 3 90
    O6 1 2.7324275 2 81.5236571 3 -90
    C7 6 2.3311086 1 84.7957223 2 -94.5926334
    O8 7 1.2469132 6 83.3453245 1 -7.8908402
    C9 4 2.3363999 1 84.8550604 2 88.0732267
    O10 9 1.2467328 4 83.3048937 1 -4.3374194
    C11 6 1.4212305 1 122.1492233 2 -83.6239069
    H12 11 1.09398 6 110.7586813 1 -137.2251156
    H13 11 1.0956905 6 111.0607388 1 101.3632461
    C14 4 1.4228241 1 122.8452116 2 95.0986151
    H15 14 1.0942462 4 110.7009151 1 -131.0133459
    H16 14 1.0953222 4 110.7959973 1 107.8525573
    N17 9 1.3232724 4 154.0341917 1 -178.2163338
    N18 7 1.3234598 6 153.8251504 1 -179.4300034
    H19 18 1.0097293 7 122.03219 6 -9.060107
    H20 18 1.0109673 7 119.6967154 6 171.4166182
    H21 17 1.0109665 9 119.643882 4 173.8079201
    H22 17 1.0097137 9 122.0917072 4 -6.5105222
    end of z-matrix
  &SEWARD 
  &SCF &End
    ITERATIONS
      300
    PRORbitals
      2 5.0
    charge
      2
&GRID_IT
ALL
NAME=ORB$L
>>>ENDDO

output

     Center  Label                x              y              z                     x              y              z
        1      U1               0.000000       0.000000       0.000000              0.000000       0.000000       0.000000
        2      O2               0.000000       0.000000       3.219236              0.000000       0.000000       1.703546
        3      X3               3.690936       0.000000       0.000000              1.953159       0.000000       0.000000
        4      X3              -3.690936       0.000000       0.000000             -1.953159       0.000000       0.000000
        5      O4               0.000000      -5.137939      -0.251997              0.000000      -2.718880      -0.133351
        6      O5               0.000000      -0.060555      -3.232714              0.000000      -0.032044     -1.710678
        7      O6               0.000000       5.107137       0.761111              0.000000       2.702581       0.402763
        8      C7              -4.372911       4.763701       0.354780             -2.314045       2.520842       0.187741

No change in coordinates， seeing Z of O2, and z of O5

Last edited by zz (2022-11-01 02:41:31)

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#2 2022-11-01 09:22:33

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

Re: Loop failure

I ran it (just with GATEWAY though) and got all the different geometries:

$ grep '2      O2' loop.log 
        2      O2               0.000000       0.000000       3.219236              0.000000       0.000000       1.703546
        2      O2               0.000000       0.000000       3.238133              0.000000       0.000000       1.713546
        2      O2               0.000000       0.000000       3.275928              0.000000       0.000000       1.733546
        2      O2               0.000000       0.000000       3.332620              0.000000       0.000000       1.763546
        2      O2               0.000000       0.000000       3.408209              0.000000       0.000000       1.803546
        2      O2               0.000000       0.000000       3.502695              0.000000       0.000000       1.853546
        2      O2               0.000000       0.000000       3.616078              0.000000       0.000000       1.913546
        2      O2               0.000000       0.000000       3.748359              0.000000       0.000000       1.983546
        2      O2               0.000000       0.000000       3.899537              0.000000       0.000000       2.063546
        2      O2               0.000000       0.000000       4.069613              0.000000       0.000000       2.153546
        2      O2               0.000000       0.000000       4.258585              0.000000       0.000000       2.253546

Are you sure you looked at the coordinates of all iterations? By the way, note that the variable modifications are cumulative, so you get the initial value +0.00, +0.01, +0.03, +0.06, +0.10, +0.15...

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#3 2022-11-01 09:36:24

zz
Member
Registered: 2022-10-17
Posts: 13

Re: Loop failure

I don't have the loop.log file output, and looking at the UO2-DGA.log file, the coordinates in it haven't changed, and the result of SCF is the same

grep "Total SCF energy" UO2-DGA.log
::    Total SCF energy                             -29079.3584424913
::    Total SCF energy                             -29079.3584424913
::    Total SCF energy                             -29079.3584424913
::    Total SCF energy                             -29079.3584424913
::    Total SCF energy                             -29079.3584424913
::    Total SCF energy                             -29079.3584424913
::    Total SCF energy                             -29079.3584424913
::    Total SCF energy                             -29079.3584424913
::    Total SCF energy                             -29079.3584424913
::    Total SCF energy                             -29079.3584424913
::    Total SCF energy                             -29079.3584424913

This also shows that the structure has not changed, right?

Last edited by zz (2022-11-01 09:40:10)

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#4 2022-11-01 09:47:54

zz
Member
Registered: 2022-10-17
Posts: 13

Re: Loop failure

this is my log file

       2      O2               0.000000       0.000000       3.219236              0.000000       0.000000       1.703546
        2      O2               0.000000       0.000000       3.219236              0.000000       0.000000       1.703546
        2      O2               0.000000       0.000000       3.219236              0.000000       0.000000       1.703546
        2      O2               0.000000       0.000000       3.219236              0.000000       0.000000       1.703546
        2      O2               0.000000       0.000000       3.219236              0.000000       0.000000       1.703546
        2      O2               0.000000       0.000000       3.219236              0.000000       0.000000       1.703546
        2      O2               0.000000       0.000000       3.219236              0.000000       0.000000       1.703546
        2      O2               0.000000       0.000000       3.219236              0.000000       0.000000       1.703546
        2      O2               0.000000       0.000000       3.219236              0.000000       0.000000       1.703546
        2      O2               0.000000       0.000000       3.219236              0.000000       0.000000       1.703546
        2      O2               0.000000       0.000000       3.219236              0.000000       0.000000       1.703546

Do I want to increase the key length evenly or can i write as following?

 >>export dist=1.691177
 >>>FOREACH L in (0,1,2,3,4,5,6,7,8,9,10)
 >>eval dist=1.691177+$L/100
  &GATEWAY

Last edited by zz (2022-11-01 09:55:39)

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#5 2022-11-02 05:09:40

zz
Member
Registered: 2022-10-17
Posts: 13

Re: Loop failure

Can you give me a input file that you succeed? Or can you provide us with your submission script? I haven't understood the reason why i failed smile

Last edited by zz (2022-11-02 08:34:22)

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#6 2022-11-02 09:48:52

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

Re: Loop failure

$ cat loop.input 
>>export dist=1.7035463
>>export bond=1.7109785
>>>FOREACH L in (0,1,2,3,4,5,6,7,8,9,10)
>>eval dist=$dist+$L/100
>>eval bond=$bond+$L/100
&GATEWAY
  TITLE
  UO2-DGA
  Symmetry
  X
  XBAS
  O.STO-3G
  *U.ANO-RCC-VTZP
  *O.ANO-RCC-VDZP
  *N.ANO-RCC-VDZ
  *H.ANO-RCC-VDZ
  *C.ANO-RCC-VDZ
  end of basis
  ZMAT
   O1
   O2 1 $dist
   O3 1 1.9531593 2 90
   O4 1 2.7221484 2 92.8078917 3 90
   O5 1 $bond 2 178.9268708 3 90
   *O6 1 2.7324275 2 81.5236571 3 -90
   *C7 6 2.3311086 1 84.7957223 2 -94.5926334
   *O8 7 1.2469132 6 83.3453245 1 -7.8908402
   *C9 4 2.3363999 1 84.8550604 2 88.0732267
   *O10 9 1.2467328 4 83.3048937 1 -4.3374194
   *C11 6 1.4212305 1 122.1492233 2 -83.6239069
   *H12 11 1.09398 6 110.7586813 1 -137.2251156
   *H13 11 1.0956905 6 111.0607388 1 101.3632461
   *C14 4 1.4228241 1 122.8452116 2 95.0986151
   *H15 14 1.0942462 4 110.7009151 1 -131.0133459
   *H16 14 1.0953222 4 110.7959973 1 107.8525573
   *N17 9 1.3232724 4 154.0341917 1 -178.2163338
   *N18 7 1.3234598 6 153.8251504 1 -179.4300034
   *H19 18 1.0097293 7 122.03219 6 -9.060107
   *H20 18 1.0109673 7 119.6967154 6 171.4166182
   *H21 17 1.0109665 9 119.643882 4 173.8079201
   *H22 17 1.0097137 9 122.0917072 4 -6.5105222
   end of z-matrix
 &SEWARD
 &SCF
>>>ENDDO

$ pymolcas -f loop.input 

$ grep '2      O2' loop.log
        2      O2               0.000000       0.000000       3.219236              0.000000       0.000000       1.703546
        2      O2               0.000000       0.000000       3.238133              0.000000       0.000000       1.713546
        2      O2               0.000000       0.000000       3.275928              0.000000       0.000000       1.733546
        2      O2               0.000000       0.000000       3.332620              0.000000       0.000000       1.763546
        2      O2               0.000000       0.000000       3.408209              0.000000       0.000000       1.803546
        2      O2               0.000000       0.000000       3.502695              0.000000       0.000000       1.853546
        2      O2               0.000000       0.000000       3.616078              0.000000       0.000000       1.913546
        2      O2               0.000000       0.000000       3.748359              0.000000       0.000000       1.983546
        2      O2               0.000000       0.000000       3.899537              0.000000       0.000000       2.063546
        2      O2               0.000000       0.000000       4.069613              0.000000       0.000000       2.153546
        2      O2               0.000000       0.000000       4.258585              0.000000       0.000000       2.253546

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#7 2022-11-29 20:38:50

valera
Administrator
Registered: 2015-11-03
Posts: 129

Re: Loop failure

if I dare to interrupt..
The description of EMIL language says: all environment variables must be upper case. So, DIST=$DIST+$L/100 is correct, but dist=$dist is not. Of course, pymolcas can handle this in a different way..

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