towhee-users Mailing List for MCCCS Towhee

Hi towhee users,

I would like to use towhee package. However, I have some difficulties to
compile the current package. When I try to compile it, I got several errors.


First, I got some error massages regarding to engatom.F:

engatom.F: In subroutine `twh_engatom':
engatom.F:26:
        &     ,lnbterm,dimatoms,dimtrials,rxp,ryp,rzp,vctry,vtrext
                                1
engatom.F:66: (continued):
         dimension lnbterm(dimtrials)
                           2
Invalid declaration of or reference to symbol `dimtrials' at (2) [initially
seen at (1)]
engatom.F:26:
        &     ,lnbterm,dimatoms,dimtrials,rxp,ryp,rzp,vctry,vtrext
                                1
After I checked engatom.F, I think I need to move "integer
dimatoms,dimtrials"  from line 70 to line 65 because we need to declare the
variable type before we use that variable. Another same type error message
suggest me move "integer dimatoms,dimtrials" from line 176 to line 171.

After these two modification, I got other error messages as:
allocate.o(.text+0x1f): In function `twh_allocate_eam__':
/home/dong/sourceFiles/towhee-6.1.4/Source/allocate.F:39: undefined
reference to `twh_eam_rho_real__'

I believe this error message is related to the hybridization of fortran code
and c code. Could you please tell me how to fix it? Thank you for your help
in advance!

Happy holiday!

Dongsheng

On Mon, Dec 22, 2008 at 7:35 AM, Babak Fazel <bk...@ya...> wrote:
> I have run towhee code with the following input file, for an NPT simulation
> of methane. Yet my results look to be significantly different from the
> corresponding experimental values. Any suggestions on the things which I
> might have missed?

Sure.  You missed performing any volume moves and therefore your
simulation is going to be at the vapor volume that you started it at.

> initlattice
> 'simple cubic'
> initmol
> 500
> inix iniy iniz
> 8    8    8
> hmatrix
> 270.0d0 0.0d0 0.0d0
> 0.0d0 270.0d0 0.0d0
> 0.0d0 0.0d0 270.0d0

That initial box size for 500 molecules is certainly a vapor.

> pm1boxcbswap
> 0.0d0
>           pm1cbswmt
>           1.0d0
> pmavb1
> 1.0d0
>           pmavb1in
>           0.5d0
>           pmavb1mt
>           1.0d0
>           pmavb1ct
>           1.0d0
>           avb1rad
>           20.0d0

By setting pmavb1 to a value of 1.0 you are only performing
Aggregation-volume bias moves of type 1.  While this is a very nice
move for sampling clusters in a vapor, it is not doing anything to
sample the volume changes.

A more typical single-box NPT simulation would consist of about 1%
volume moves, perhaps 5% of each of the aggregation volume bias moves,
and the remainder broken up between CBMC, translation, and rotation
moves.  As you are simulating a monatomic molecule in this particular
case there is no need for CBMC or rotation moves.

Marcus
-- 
Marcus G. Martin
Director, Useful Bias Incorporated
88 Martinez Road
Edgewood NM 87015-8222
ph. (505) 286-4457
www.usefulbias.com
www.photobirder.com

On Mon, Dec 22, 2008 at 2:44 AM, naresh nitt <nar...@gm...> wrote:
> Dear Towhee users,
>        I want to run a GCMC simulation by having the adsorbing molecule to
> be a rigid molecule.
>        Is there any way to run a simulation of this sort.

If the force field for the molecule is rigid then there is now no
problem in running this sort of simulation in the newest versions of
the code.

If you are using a force field that is flexible, but for some reason
feel the need to keep the molecule rigid then GCMC will not work.  The
only way to do something like that would be a 2-box Gibbs ensemble
simulation using only the rotational-bias moves.

Marcus

-- 
Marcus G. Martin
Director, Useful Bias Incorporated
88 Martinez Road
Edgewood NM 87015-8222
ph. (505) 286-4457
www.usefulbias.com
www.photobirder.com

I just wanted to post the following question to the Towhee community, which
was sent by a friend mine. Hope someone can help.

I have run towhee code with the following input file, for an NPT simulation
of methane. Yet my results look to be significantly different from the
corresponding experimental values. Any suggestions on the things which I
might have missed?
Towhee:                                                     Experiment:
Specific Density   (g/ml)   0.00067672          Specific Density   (g/ml)
0.43825
Internal Enegry (KJ/mol)  -0.1131E+2           Internal Enegry
(KJ/mol) -0.603

 (Exp. Data Ref:
http://webbook.nist.gov/cgi/fluid.cgi?T=101&PLow=1&PHigh=1&PInc=1&Digits=5&ID=C74828&Action=Load&Type=IsoTherm&TUnit=K&PUnit=MPa&DUnit=g%2Fml&HUnit=kJ%2Fmol&WUnit=m%2Fs&VisUnit=uPa*s&STUnit=N%2Fm&RefState=DEF
)

--------------------------------------------------------------------------------------------------------------------------
inputformat
'Towhee'
randomseed
1302002
random_luxlevel
3
random_allow_restart
T
ensemble
'npt'
temperature
101
pressure
1000.d0
nmolty
1
nmolectyp
500
numboxes
1
stepstyle
'cycles'
nstep
10
printfreq
1
blocksize
2
moviefreq
100
backupfreq
1000
runoutput
'full'
pdb_output_freq
5
loutdft
.false.
loutlammps
.false.
pressurefreq
2
trmaxdispfreq
1000
volmaxdispfreq
1000
chempotperstep
0
potentialstyle
'internal'
ffnumber
1
ff_filename
/home/Bobby/usr/packages/towhee-6.0.4/ForceFields/towhee_ff_TraPPE-UA
classical_potential
'Lennard-Jones'
classical_mixrule
'Lorentz-Berthelot'
lshift
.false.
ltailc
.true.
rmin
1.0d0
rcut
20.0d0
rcutin
5.0d0
electrostatic_form
'none'
nfield
0
solvation_style
'none'
linit
.true.
initboxtype
'dimensions'
initstyle
'full cbmc'
initlattice
'simple cubic'
initmol
500
inix iniy iniz
8    8    8
hmatrix
270.0d0 0.0d0 0.0d0
0.0d0 270.0d0 0.0d0
0.0d0 0.0d0 270.0d0
pm1boxcbswap
0.0d0
          pm1cbswmt
          1.0d0
pmavb1
1.0d0
          pmavb1in
          0.5d0
          pmavb1mt
          1.0d0
          pmavb1ct
          1.0d0
          avb1rad
          20.0d0
pmavb2
0.0d0
          pmavb2in
          0.5d0
          pmavb2mt
          1.0d0
          pmavb2ct
          1.0d0
          avb2rad
          10.0d0
pmavb3
0.0d0
          pmavb3mt
          1.0d0
          pmavb3ct
          1.0d0
          avb3rad
          10.0d0
pmcb
0.0d0
          pmcbmt
          1.0d0
          pmall
          0.0d0
pmback
0.0d0
          pmbkmt
          1.0d0
pmpivot
0.0d0
          pmpivmt
          1.0d0
pmconrot
0.0d0
          pmcrmt
          1.0d0
pmcrback
0.0d0
          pmcrbmt
          1.0d0
pmplane
0.0d0
          pmplanebox
          1.0d0
          planewidth
          3.0d0
pmrow
0.0d0
          pmrowbox
          1.0d0
          rowwidth
          3.0d0
pmtraat
0.0d0
          pmtamt
          1.0d0
          rmtraa
          0.5d0
          tatraa
          0.5d0
pmtracm
1.0d0
          pmtcmt
          1.0d0
          rmtrac
          0.5d0
          tatrac
          0.5d0
pmrotate
1.0d0
          pmromt
          1.0d0
          rmrot
          0.05d0
          tarot
          0.5d0
cbmc_style
'coupled-decoupled'
coupled_decoupled_form
'Martin and Siepmann JPCB 1999'
cbmc_setting_style
'default ideal'
#trappe-ua methane
input_style
'basic connectivity map'
nunit
1
nmaxcbmc
1
lpdbnames
F
forcefield
'TraPPE-UA'
charge_assignment
'manual'
unit ntype qqatom
1    'CH4'   0.0d0
vibration
0
improper
0
---------------------------------------------------------------------------------------------------------------------------------

I have run towhee code with the following input file, for an NPT simulation of methane. Yet my results look to be significantly different from the corresponding experimental values. Any suggestions on the things which I might have missed?
 
 
 
 
 
Towhee:                                                     Experiment: 
Specific Density   (g/ml)   0.00067672          Specific Density   (g/ml)  0.43825
Internal Enegry (KJ/mol)  -0.1131E+2           Internal Enegry (KJ/mol) -0.603
 
 (Exp. Data Ref: http://webbook.nist.gov/cgi/fluid.cgi?T=101&PLow=1&PHigh=1&PInc=1&Digits=5&ID=C74828&Action=Load&Type=IsoTherm&TUnit=K&PUnit=MPa&DUnit=g%2Fml&HUnit=kJ%2Fmol&WUnit=m%2Fs&VisUnit=uPa*s&STUnit=N%2Fm&RefState=DEF)
 
--------------------------------------------------------------------------------------------------------------------------
inputformat
'Towhee'
randomseed
1302002
random_luxlevel
3
random_allow_restart
T
ensemble
'npt'
temperature
101
pressure
1000.d0
nmolty
1
nmolectyp
500
numboxes
1
stepstyle
'cycles'
nstep
10
printfreq
1   
blocksize
2
moviefreq
100
backupfreq
1000
runoutput
'full'
pdb_output_freq
5
loutdft 
..false.  
loutlammps
..false.
pressurefreq
2
trmaxdispfreq
1000
volmaxdispfreq
1000
chempotperstep
0
potentialstyle
'internal'
ffnumber
1
ff_filename
/home/Bobby/usr/packages/towhee-6.0.4/ForceFields/towhee_ff_TraPPE-UA
classical_potential
'Lennard-Jones'       
classical_mixrule
'Lorentz-Berthelot'
lshift
..false.
ltailc
..true.
rmin  
1.0d0 
rcut  
20.0d0
rcutin 
5.0d0 
electrostatic_form
'none'
nfield
0
solvation_style
'none'
linit   
..true. 
initboxtype
'dimensions'
initstyle
'full cbmc'
initlattice
'simple cubic'
initmol
500
inix iniy iniz
8    8    8
hmatrix
270.0d0 0.0d0 0.0d0
0.0d0 270.0d0 0.0d0
0.0d0 0.0d0 270.0d0 
pm1boxcbswap    
0.0d0     
          pm1cbswmt
          1.0d0
pmavb1
1.0d0
          pmavb1in
          0.5d0
          pmavb1mt
          1.0d0
          pmavb1ct
          1.0d0
          avb1rad
          20.0d0
pmavb2
0.0d0
          pmavb2in
          0.5d0
          pmavb2mt
          1.0d0
          pmavb2ct
          1.0d0
          avb2rad
          10.0d0
pmavb3
0.0d0
          pmavb3mt
          1.0d0
          pmavb3ct
          1.0d0
          avb3rad
          10.0d0
pmcb      
0.0d0     
          pmcbmt
          1.0d0
          pmall
          0.0d0 
pmback
0.0d0
          pmbkmt
          1.0d0
pmpivot
0.0d0
          pmpivmt
          1.0d0
pmconrot
0.0d0
          pmcrmt
          1.0d0
pmcrback
0.0d0
          pmcrbmt
          1.0d0
pmplane
0.0d0
          pmplanebox
          1.0d0
          planewidth
          3.0d0
pmrow
0.0d0
          pmrowbox
          1.0d0
          rowwidth
          3.0d0
pmtraat   
0.0d0   
          pmtamt
          1.0d0
          rmtraa
          0.5d0 
          tatraa
          0.5d0
pmtracm   
1.0d0   
          pmtcmt
          1.0d0
          rmtrac
          0.5d0 
          tatrac 
          0.5d0
pmrotate
1.0d0
          pmromt  
          1.0d0
          rmrot
          0.05d0
          tarot
          0.5d0
cbmc_style
'coupled-decoupled'
coupled_decoupled_form
'Martin and Siepmann JPCB 1999'
cbmc_setting_style
'default ideal'
#trappe-ua methane
input_style
'basic connectivity map'
nunit
1
nmaxcbmc
1
lpdbnames
F
forcefield
'TraPPE-UA'
charge_assignment
'manual'
unit ntype qqatom
1    'CH4'   0.0d0
vibration
0
improper
0
---------------------------------------------------------------------------------------------------------------------------------
 
             
 


      

Dear Towhee users,
       I want to run a GCMC simulation by having the adsorbing molecule to
be a rigid molecule.
       Is there any way to run a simulation of this sort.

Thanks in advance
Naresh

Hello Towhee-users,

I am once again gutting and rebuilding the internal data structures in
Towhee (more on that in a minute), and this leads to a surprising
amount of work continuing to try and keep the 'database' inputformat
option functional.  I implemented that format for my own purposes many
years ago, but no longer use it myself.  If anyone out there uses this
functionality let me know soon as otherwise I am likely to scrap it to
save myself the bother of continuing to maintain something of minimal
use.

The data structure changes are happening because I am replacing the
static declared arrays in the data structures with run-time allocation
of memory (in C functions that replace the subroutines currently in
globaldata.F).  Yes, the goal is the elimination of those
not-so-lovely #defined array dimensions in preproc.h.  The first
installment of the new functionality will come with the next release
and there will likely be a period of instability in the code until the
transition is complete and fully debugged.  I appreciate your patience
and your prompt and detailed bug reports during the next few releases
of Towhee.

thanks,

Marcus

-- 
Marcus G. Martin
Director, Useful Bias Incorporated
88 Martinez Road
Edgewood NM 87015-8222
ph. (505) 286-4457
www.usefulbias.com
www.photobirder.com