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#1 2016-03-10 18:06:20
- wangjun
- Member
- Registered: 2015-12-09
- Posts: 26
error to read mass-weighed velocities in dynamics
For the dynamics, when I try to use the mass-weighed velocities (unit is sqrt(amu)*bohr/sec), I set the keyword VELO= 2 and copy the velocity file '>> COPY $CurrDir/$Project.velocity.xyz .' . And the error is
()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
MOLCAS executing module DYNAMIX with 15000 MB of memory
at 21:46:10 Wed Mar 9 2016
()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
***
*** NuclearChargeBySymbol: error
*** unknown atom: ^@^@
***
***
*** NuclearChargeBySymbol: error
*** unknown atom: ^@^@
***
***
*** NuclearChargeBySymbol: error
*** unknown atom: ^@^@
***
***
*** NuclearChargeBySymbol: error
*** unknown atom: ^@^@
***
***
*** NuclearChargeBySymbol: error
*** unknown atom: ^@^@
***
***
*** NuclearChargeBySymbol: error
*** unknown atom: ^@^@
***
***
*** NuclearChargeBySymbol: error
*** unknown atom: ^@^@
***
***
*** NuclearChargeBySymbol: error
*** unknown atom: ^@^@
***
****** NuclearChargeBySymbol: error
*** unknown atom: ^@^@
***
******
***
*** NuclearChargeBySymbol: error
*** unknown atom: ^@^@
***
***
*** NuclearChargeBySymbol: error
*** unknown atom: ^@^@
***
***
*** NuclearChargeBySymbol: error
*** unknown atom: ^@^@
***
***
*** NuclearChargeBySymbol: error
*** unknown atom: ^@^@
***
***
*** NuclearChargeBySymbol: error
*** unknown atom: ^@^@
***
The initial mass weighted velocities (bohr/au) are read in.
The initial kinetic energy (Hartree) is: 0.15648358D+28
The initial total energy (Hartree) is: 0.15648358D+28
*** First step of the Velocity Verlet algorithm ***
Old Coordinates (time= 0.0a.u.):
--------------------------------------------
No. Atom X Y Z
--------------------------------------------
1 C -5.718179 -2.297155 0.371318 0.00D+00 -0.29606D-02 0.21495D-01 -0.23050D-02
2 C -3.397915 1.466208 -0.110944 0.00D+00 0.40722D-01 0.25495D-01 -0.55825D-02
3 C -1.511337 -0.477676 0.012829 0.00D+00 -0.54162D-01 -0.86702D-02 -0.85007D-03
4 C -2.906076 -3.000655 0.092687 0.00D+00 -0.21246D-02 -0.18448D-02 0.28650D-02
5 C 1.070001 -0.249147 -0.078399 0.00D+00 0.69490D-01 -0.15340D-01 -0.63311D-03
6 C 2.599093 -2.516854 -0.178490 0.00D+00 -0.51965D-01 0.61532D-02 0.51424D-03
7 C 2.476692 2.233758 -0.196906 0.00D+00 -0.11995D-02 0.65927D-02 0.43084D-03
8 C 5.148109 -2.439281 -0.357481 0.00D+00 0.45891D-01 -0.43748D-02 -0.33027D-02
9 C 5.074041 2.021013 1.043820 0.00D+00 -0.13428D-03 0.46332D-02 0.43519D-02
10 H 2.723267 2.746524 -2.186545 0.00D+00 -0.23512D-02 0.96760D-03 0.33981D-02
11 H 1.418294 3.751583 0.698545 0.00D+00 0.34415D-02 -0.70164D-02 -0.32411D-02
12 C 6.625733 -0.035859 -0.246564 0.00D+00 0.37061D-02 0.27953D-02 0.31579D-02
13 H 6.034869 3.844124 0.974526 0.00D+00 -0.12487D-02 -0.63419D-02 -0.90252D-03
14 H 4.823148 1.536325 3.031459 0.00D+00 0.19439D-02 0.21226D-02 -0.24651D-02
15 H 8.421978 -0.343592 0.719863 0.00D+00 -0.44154D-02 -0.17452D-02 -0.27976D-02
16 H 7.113745 0.551348 -2.170830 0.00D+00 -0.88926D-03 -0.37353D-02 0.11834D-02
17 H -6.941410 -3.148616 -1.042940 0.00D+00 0.39205D-02 -0.13491D-02 0.27556D-02
18 H 6.194454 -4.195237 -0.567247 0.00D+00 -0.57189D-02 0.65791D-02 0.32201D-03
19 H 1.656453 -4.339093 -0.200509 0.00D+00 0.62850D-02 0.83589D-02 0.34267D-03
20 H -2.286128 -4.178957 1.658460 0.00D+00 -0.83337D-03 0.12940D-02 -0.24377D-02
21 H -2.594428 -4.059691 -1.643476 0.00D+00 -0.24648D-03 0.13107D-02 0.18287D-02
22 H -6.483442 -2.714312 2.233377 0.00D+00 0.28731D-02 -0.33332D-02 -0.21620D-02
23 H -7.276355 1.518042 -0.049074 0.00D+00 0.20007D-01 -0.15019D-01 0.17541D-02
24 C -3.147088 4.265397 -0.383395 0.00D+00 0.46923D-02 0.60343D-03 0.18721D-02
25 H -2.405300 5.077316 1.353137 0.00D+00 -0.28348D-02 0.41522D-02 -0.22941D-02
26 H -1.864744 4.743740 -1.912684 0.00D+00 -0.36296D-02 0.26495D-02 0.11587D-02
27 H -4.977900 5.116133 -0.762860 0.00D+00 0.36950D-02 -0.71946D-03 -0.17951D-03
28 N -5.665989 0.457839 0.017429 0.00D+00 -0.71954D-01 -0.25713D-01 0.32177D-02
--------------------------------------------
Molecular Dynamics specifications (time = 0.0a.u.)
========================================== Kinetic energy 0.1565D+28 a.u.
Total linear momentum 0.4149D+15 a.u.
RMS deviation 0.3801D+13 Bohr
New Coordinates (time= 40.0a.u.):
--------------------------------------------
No. Atom X Y Z
--------------------------------------------
1 C ********************************* 0.22D+05 -0.29606D-02 0.21495D-01 -0.23050D-02
2 C ********************************* 0.22D+05 0.40722D-01 0.25495D-01 -0.55825D-02
3 C ********************************* 0.22D+05 -0.54162D-01 -0.86702D-02 -0.85007D-03
4 C ********************************* 0.22D+05 -0.21246D-02 -0.18448D-02 0.28650D-02
5 C ********************************* 0.22D+05 0.69490D-01 -0.15340D-01 -0.63311D-03
6 C ********************************* 0.22D+05 -0.51965D-01 0.61532D-02 0.51424D-03
7 C ********************************* 0.22D+05 -0.11995D-02 0.65927D-02 0.43084D-03
8 C ********************************* 0.22D+05 0.45891D-01 -0.43748D-02 -0.33027D-02
9 C ********************************* 0.22D+05 -0.13428D-03 0.46332D-02 0.43519D-02
10 H ********************************* 0.18D+04 -0.23512D-02 0.96760D-03 0.33981D-02
11 H ********************************* 0.18D+04 0.34415D-02 -0.70164D-02 -0.32411D-02
12 C ********************************* 0.22D+05 0.37061D-02 0.27953D-02 0.31579D-02
13 H ********************************* 0.18D+04 -0.12487D-02 -0.63419D-02 -0.90252D-03
14 H ********************************* 0.18D+04 0.19439D-02 0.21226D-02 -0.24651D-02
15 H ********************************* 0.18D+04 -0.44154D-02 -0.17452D-02 -0.27976D-02
16 H ********************************* 0.18D+04 -0.88926D-03 -0.37353D-02 0.11834D-02
17 H ********************************* 0.18D+04 0.39205D-02 -0.13491D-02 0.27556D-02
18 H ********************************* 0.18D+04 -0.57189D-02 0.65791D-02 0.32201D-03
19 H ********************************* 0.18D+04 0.62850D-02 0.83589D-02 0.34267D-03
20 H ********************************* 0.18D+04 -0.83337D-03 0.12940D-02 -0.24377D-02
21 H ********************************* 0.18D+04 -0.24648D-03 0.13107D-02 0.18287D-02
22 H ********************************* 0.18D+04 0.28731D-02 -0.33332D-02 -0.21620D-02
23 H ********************************* 0.18D+04 0.20007D-01 -0.15019D-01 0.17541D-02
24 C ********************************* 0.22D+05 0.46923D-02 0.60343D-03 0.18721D-02
25 H ********************************* 0.18D+04 -0.28348D-02 0.41522D-02 -0.22941D-02
26 H ********************************* 0.18D+04 -0.36296D-02 0.26495D-02 0.11587D-02
27 H ********************************* 0.18D+04 0.36950D-02 -0.71946D-03 -0.17951D-03
28 N ********************************* 0.26D+05 -0.71954D-01 -0.25713D-01 0.32177D-02
--------------------------------------------
The velocity is Kinetic energy 0.1565D+28 a.u.
Total linear momentum 0.4149D+15 a.u.
RMS deviation 0.3801D+13 Bohr
New Coordinates (time= 40.0a.u.):
--------------------------------------------
No. Atom X Y Z
--------------------------------------------
1 C ********************************* 0.22D+05 -0.29606D-02 0.21495D-01 -0.23050D-02
2 C ********************************* 0.22D+05 0.40722D-01 0.25495D-01 -0.55825D-02
3 C ********************************* 0.22D+05 -0.54162D-01 -0.86702D-02 -0.85007D-03
4 C ********************************* 0.22D+05 -0.21246D-02 -0.18448D-02 0.28650D-02
5 C ********************************* 0.22D+05 0.69490D-01 -0.15340D-01 -0.63311D-03
6 C ********************************* 0.22D+05 -0.51965D-01 0.61532D-02 0.51424D-03
7 C ********************************* 0.22D+05 -0.11995D-02 0.65927D-02 0.43084D-03
8 C ********************************* 0.22D+05 0.45891D-01 -0.43748D-02 -0.33027D-02
9 C ********************************* 0.22D+05 -0.13428D-03 0.46332D-02 0.43519D-02
10 H ********************************* 0.18D+04 -0.23512D-02 0.96760D-03 0.33981D-02
11 H ********************************* 0.18D+04 0.34415D-02 -0.70164D-02 -0.32411D-02
12 C ********************************* 0.22D+05 0.37061D-02 0.27953D-02 0.31579D-02
13 H ********************************* 0.18D+04 -0.12487D-02 -0.63419D-02 -0.90252D-03
14 H ********************************* 0.18D+04 0.19439D-02 0.21226D-02 -0.24651D-02
15 H ********************************* 0.18D+04 -0.44154D-02 -0.17452D-02 -0.27976D-02
16 H ********************************* 0.18D+04 -0.88926D-03 -0.37353D-02 0.11834D-02
17 H ********************************* 0.18D+04 0.39205D-02 -0.13491D-02 0.27556D-02
18 H ********************************* 0.18D+04 -0.57189D-02 0.65791D-02 0.32201D-03
19 H ********************************* 0.18D+04 0.62850D-02 0.83589D-02 0.34267D-03
20 H ********************************* 0.18D+04 -0.83337D-03 0.12940D-02 -0.24377D-02
21 H ********************************* 0.18D+04 -0.24648D-03 0.13107D-02 0.18287D-02
22 H ********************************* 0.18D+04 0.28731D-02 -0.33332D-02 -0.21620D-02
23 H ********************************* 0.18D+04 0.20007D-01 -0.15019D-01 0.17541D-02
24 C ********************************* 0.22D+05 0.46923D-02 0.60343D-03 0.18721D-02
25 H ********************************* 0.18D+04 -0.28348D-02 0.41522D-02 -0.22941D-02
26 H ********************************* 0.18D+04 -0.36296D-02 0.26495D-02 0.11587D-02
27 H ********************************* 0.18D+04 0.36950D-02 -0.71946D-03 -0.17951D-03
28 N ********************************* 0.26D+05 -0.71954D-01 -0.25713D-01 0.32177D-02
--------------------------------------------How to solve this problem?
Thanks in advance!
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#2 2016-04-14 10:38:02
- Alessio Valentini
- Member
- Registered: 2015-11-09
- Posts: 6
Re: error to read mass-weighed velocities in dynamics
Sorry for this huge delay....
Can I see the velocity.xyz file and the input file?
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#3 2016-04-21 14:41:14
- wangjun
- Member
- Registered: 2015-12-09
- Posts: 26
Re: error to read mass-weighed velocities in dynamics
the velocity.xyz is just like this:
2.325618845956D+12 4.121018311439D+12 6.288475315270D+11
6.704821727289D+11 1.347722001622D+12 1.394776094807D+12
-7.004666834881D+11 -2.962719725496D+11 2.045726675622D+12
-6.319658283163D+11 -8.383542643175D+11 1.192881801799D+11
6.985311313428D+11 3.985345179740D+12 -3.189319166002D+12
-5.375325581280D+11 -8.107847930558D+11 1.755823503938D+12
7.976878744801D+11 -1.012592207406D+12 -2.699265827981D+11
2.196939344553D+12 3.010073119287D+12 -1.439686970141D+12
-2.804474354707D+12 -3.326710604574D+12 2.374121663854D+12
-8.745851634328D+11 -4.377372137624D+12 -5.471496127802D+12
4.228995401352D+11 2.802956576476D+12 -3.766021612615D+12
-3.016229323380D+12 1.163929472029D+11 -1.112138437201D+11
-1.636527893386D+11 8.550337027872D+11 6.241181873377D+12
-4.080497565189D+12 -5.811425451132D+12 2.666032084813D+12
2.066344873042D+12 -1.419850802499D+12 -2.373603712019D+12
-2.827949200331D+12 -2.072043130231D+12 -5.317642895386D+12
-7.012252489904D+11 -6.146606188283D+11 -3.908169279121D+11
-1.361583799274D+12 -1.052557133330D+10 1.746411414269D+12
3.309190238861D+12 -8.162932600633D+11 2.090404985916D+12
2.983533156436D+11 -2.711277700958D+12 4.663801910378D+11
3.949788684462D+11 -7.044789077904D+10 -3.098407336087D+12
5.107265768794D+11 1.292605178684D+12 2.933218189900D+12
-2.050240514159D+12 8.897729795085D+10 -5.616132215119D+11
-1.897558374736D+12 1.764536116845D+12 -1.391979661218D+12
-2.221816814523D+11 2.563782398699D+11 3.061379692250D+12
2.898201093187D+12 1.121571404225D+12 -2.621166979230D+11
-1.398735145553D+12 3.812915481846D+12 -1.770765819016D+12
3.697697442024D+12 -5.403036637079D+12 -7.526478527534D+11the input is
&GATEWAY
COORD = stru.xyz
BASIS= ano-l-vdzp
GROUP= nosym
RICD
>> FOREACH ITER in (1 .. 600)
&SEWARD
DoAnalytical
>> IF ( $ITER = 1 )
&RASSCF
LUMORB
FileOrb= $Project.GssOrb
Symmetry= 1
Spin= 1
nActEl= 6 0 0
Inactive= 41
RAS2= 6
CIroot= 2 2 1
>> COPY $Project.JobIph $Project.JobOld
>> ENDIF
&RASSCF
JOBIPH; CIRESTART
Symmetry= 1
Spin= 1
nActEl= 6 0 0
Inactive= 41
RAS2= 6
CIroot= 2 2 1
MDRLXR= 2
>> COPY $Project.JobIph $Project.JobOld
&ALASKA
>> COPY $CurrDir/$Project.velocity.xyz .
&DYNAMIX
VELVer
DT= 40.0
VELO= 2
THER= 0
HOP= 1
>> END DOThanks you in advance!
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#4 2016-05-02 16:38:19
- Ignacio
- Administrator
- From: Uppsala
- Registered: 2015-11-03
- Posts: 1,204
Re: error to read mass-weighed velocities in dynamics
wangjun wrote:
For the dynamics, when I try to use the mass-weighed velocities (unit is sqrt(amu)*bohr/sec)
Umm... The documentation says sqrt(amu)*Bohr/(a.u. of time). By using seconds you are getting huge numbers. Where did you get "velocity.xyz" from?
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#5 2016-05-11 13:51:25
- wangjun
- Member
- Registered: 2015-12-09
- Posts: 26
Re: error to read mass-weighed velocities in dynamics
from the gaussian output
Ignacio wrote:
wangjun wrote:For the dynamics, when I try to use the mass-weighed velocities (unit is sqrt(amu)*bohr/sec)
Umm... The documentation says sqrt(amu)*Bohr/(a.u. of time). By using seconds you are getting huge numbers. Where did you get "velocity.xyz" from?
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