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From: Marcus M. <me...@gm...> - 2025-05-06 14:07:19
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Howdy Towhee users, I am planning on creating and releasing a series of video lectures related to Monte Carlo molecular simulation this fall and thought this group would be a great place to see what sort of topics I should cover. I have several ideas of what I want to talk about, but I don't want to lead the witness so I was hoping to get ideas from the community first and then combine those to come up with a list of topics. What aspect of Monte Carlo molecular simulation do you still find confusing, or have found confusing as you were getting started? Please feel free to respond either to the whole list, or to me directly ( me...@gm...). thanks, Marcus -- Marcus G. Martin 88 Martinez Road Edgewood NM 87015-8222 (505) 363 3179 www.photobirder.com towhee.sourceforge.net |
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From: Redouane R. <red...@um...> - 2022-04-04 22:30:54
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MCCCS Towhee - Version 8.2.3 (July 22 2021) Copyright (C) <2000-2021> Marcus G. Martin Code Contributors for 2021: Marcus G. Martin; Code Contributors for 2020: Marcus G. Martin; Code Contributors for 2019: Marcus G. Martin; Code Contributors for 2018: Marcus G. Martin; Code Contributors for 2017: Marcus G. Martin; Code Contributors for 2016: Marcus G. Martin; Code Contributors for 2015: Marcus G. Martin; Code Contributors for 2014: Marcus G. Martin; Code Contributors for 2013: Wesley Emeneker; Marcus G. Martin; Code Contributors for 2012: Marcus G. Martin; Code Contributors for 2011: Fred James; Marcus G. Martin; Suleiman Oloriegbe; Code Contributors for 2010: Rene Haber; Andrej Lajovic; Marcus G. Martin; Loukas Peristeras; Code Contributors for 2009: Rene Haber; Marcus G. Martin; Loukas Peristeras; Code Contributors for 2008: Rene Haber; Iyad A. Hijazi; Marcus G. Martin; Loukas Peristeras; Craig Tenney; Code Contributors for 2007: Bernhard Eckl; Frank Heilmann; Jianhui Li; Marcus G. Martin; Craig M. Tenney; Ozgur Yazaydin Code Contributors for 2006: Alan A. Chen; Arben Jusufi; Christian D. Lorenz; Marcus G. Martin; Jeffrey J. Potoff; Vincent K. Shen; Matthew A. Wyczalkowski; Ozgur Yazaydin Code Contributors for 2005: Marcus G. Martin; Alan A. Chen; Christian D. Lorenz; Matthew A. Wyczalkowski Code Contributors for 2004: Marcus G. Martin; Christian D. Lorenz; Peter A. Schultz; Aidan P. Thompson; Jeffrey J. Potoff; Steve R. Lustig; Paul S. Crozier; Nicholas du Preez Code Contributors for 2003: Marcus G. Martin; Christian D. Lorenz; David B. Ritch; Michael L. Greenfield; Yogesh Srivastava; Evangelos A Coutsias Code Contributors for 2002: Marcus G. Martin; Christian D. Lorenz; Aidan P. Thompson; Allen G. Sault Code Contributors for 2001: Marcus G. Martin Code Contributors for 2000: Marcus G. Martin Copyright (C) <1999> J. Ilja Siepmann and Marcus G. Martin Code Contributors for 1999: J. Ilja Siepmann; Marcus G. Martin; Bin Chen; Collin D. Wick; John Stubbs Direct comments about this code to Marcus G. Martin ( mar...@us...) See the MCCCS Towhee web site for more information and the users manual. http://towhee.sourceforge.net We would like to thank the following agencies for providing funding used to develop MCCCS Towhee -Department of Energy Industrial Technologies Program (MGM) -National Science Foundation (JIS) -Department of Energy Computational Science Graduate Fellowship (MGM,CDW) This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Reading from towhee_input file: Examples/DFT_Field/towhee_input in directory: current directory inputformat: Towhee Mismatch of strings in readtowhee Expected String: ensemble Found String: randomseed Fatal error, quitting. |
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From: Marcus M. <me...@gm...> - 2020-03-02 23:32:05
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Howdy towhee users, Uploaded a minor bug fix version of Towhee to SourceForge today as version 8.1.2. This was a result of myself setting up a new machine for Towhee development. I am attempting to make more time to work on Towhee each week so for those of you who still have questions or bug reports that I have not addressed please feel free to directly email me again to remind me as I attempt to work through the backlog of Towhee related questions and requests. thanks, Marcus -- Marcus G. Martin 88 Martinez Road Edgewood NM 87015-8222 land (505) 286 4457 cell (505) 363 3179 www.photobirder.com towhee.sourceforge.net |
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From: Sonibare, K. <kas...@st...> - 2018-08-16 17:07:52
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Dear towhee users, I have used towhee version 4.6.3 to set up my simulation system and plan to transfer to LAMMPS in order to perform some calculations. I am using the August 2017 version of LAMMPS. Please can anyone tell me the best way to handle this transfer? Are there forcefield changes and compatibility issues that I should be aware of? Thank you very much. |
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From: Marcus M. <mar...@us...> - 2018-03-29 22:47:09
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Howdy Towhee-users, Version 8.0.0 of Towhee is now available. This is mainly an ease of use release. The towhee_input file has been rearranged a bit and many of the parameters are now optional with defaults that should be adequate for most simulations. The web manual was edited for both style and content and I sincerely hope the new towhee_input file and manual are more readable than before. Please feel free to bring any typos or broken links in the manual to my attention (with the notable exception of non-current version towhee_input manual pages as those are not maintained). Marcus -- Marcus G. Martin 88 Martinez Road Edgewood NM 87015-8222 land (505) 286 4457 cell (505) 363 3179 www.photobirder.com towhee.sourceforge.net |
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From: Marcus M. <me...@gm...> - 2017-12-21 18:54:36
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On Thu, Dec 21, 2017 at 10:57 AM, Frank Zack via Towhee-users < tow...@li...> wrote: > I want to use towhee to compute a pase diagram of a simple metal. > Unfortunately, I don't have a force-field in towhee's format. > I only have an eam-potential file in setfl format. > > Now, I've found a file in the source folder called ffreadsetflfile.F > I'm wondering if this is a stand-alone tool or if this is somehow included > into the towhee binary... > The documentation is not helpful at all...searching for serfl doesn't give > any results. > > How to use readsetfl? > Those functions are in the forcefield utility. http://towhee.sourceforge.net/utils/forcefield.html The documentation is still fairly lacking for that feature as it primarily exists for more expert users to convert the files. Hopefully that can get you started though and then it is just a matter of making sure the file you have is the right format for the converter. You'll need to dig into the source code a bit if it doesn't just happen to work out the first time, but should get you a lot closer than having to write your own conversion utility from scratch. Marcus -- Marcus G. Martin 88 Martinez Road Edgewood NM 87015-8222 land (505) 286 4457 cell (505) 363 3179 www.photobirder.com towhee.sourceforge.net |
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From: Frank Z. <fra...@ya...> - 2017-12-21 16:57:29
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I want to use towhee to compute a pase diagram of a simple metal. Unfortunately, I don't have a force-field in towhee's format.I only have an eam-potential file in setfl format. Now, I've found a file in the source folder called ffreadsetflfile.FI'm wondering if this is a stand-alone tool or if this is somehow included into the towhee binary...The documentation is not helpful at all...searching for serfl doesn't give any results. How to use readsetfl? |
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From: Thaer Al-J. <tha...@po...> - 2017-02-13 17:01:48
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Dear Seunghwan Baek,
I had the same mistake before. I still believe there is a mistake in your force field files.
I suggest to check the Torsion Style ,Torsion Coefficients, Angle Style and Angle Coefficients in your force field fie for each component. Then try to calculate the chemical potentials for each single component in one box NPT, it should give you in the output file as fallow
Initial Energies for Box 1
Total molecules in this box 200
Molecules of type 1 : 200
total vibration 0.000 [K] 0.00000 [kcal/mol]
regular 0.000 [K] 0.00000 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 0.000 [K] 0.00000 [kcal/mol]
regular 0.000 [K] 0.00000 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 0.000 [K] 0.00000 [kcal/mol]
regular 0.000 [K] 0.00000 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -0.009 [K] -0.00002 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond 0.000 [K] 0.00000 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -0.009 [K] -0.00002 [kcal/mol]
total coulombic 0.000 [K] 0.00000 [kcal/mol]
real space 0.000 [K] 0.00000 [kcal/mol]
intramolec. 0.000 [K] 0.00000 [kcal/mol]
intermolec. 0.000 [K] 0.00000 [kcal/mol]
self 0.000 [K] 0.00000 [kcal/mol]
correction 0.000 [K] 0.00000 [kcal/mol]
recip sum 0.000 [K] 0.00000 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -0.00940678 [K] -0.0000186933 [kcal/mol]
initial virial pressure in box 1 = 0.01
Best regards
Thaer Al-Jadir
PhD Student and Teaching assistant at the School of Chemical Engineering and Analytical Science | The University of Manchester | The Mill (B9) | Oxford Road | Manchester | M13 9PL | Tel: 07473889191
________________________________
From: 백승환 <kar...@na...>
Sent: 07 February 2017 16:10:06
To: Thaer Al-Jadir; tow...@li...
Subject: Re: [Towhee-users] Chemical potential calculation with multicomponents
Thank you for the email, Al-Jadir,
I do not know there is a mistake in a force field. The "towhee_ff_TraPPE-UA" is what I have used.
I did not change anything in the file, of course.
Even when I tried with only n-dodencae, it resulted in the positive value of chemical potential.
I attahced a part of my input file below.
I would appreciate any comments for this.
Best regards,
inputformat
'Towhee'
ensemble
'npt'
temperature
353.0d0
pressure
3447.38d0
nmolty
7
nmolectyp
502 96 54 30 19 13 92
numboxes
1
stepstyle
'cycles'
nstep
20000
printfreq
2000
blocksize
4000
moviefreq
4000
backupfreq
4000
runoutput
'full'
pdb_output_freq
4000
pressure_virial_freq
10
trmaxdispfreq
40
volmaxdispfreq
40
chempotperstep
10 20 30 40 50 60 120
potentialstyle
'internal'
ffnumber
1
ff_filename
/location/towhee-7.2.0/ForceFields/towhee_ff_TraPPE-UA
classical_potential
'Lennard-Jones'
classical_mixrule
'Lorentz-Berthelot'
lshift
.false.
ltailc
.true.
rmin
1.0d0
rcut
13.8d0
rcutin
10.0d0
electrostatic_form
'none'
linit
F
initboxtype
'dimensions'
initstyle
'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc'
initlattice
'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic'
initmol
502 96 54 30 19 13 92
inix iniy iniz
10 10 10
hmatrix
80.0d0 0.0d0 0.0d0
0.0d0 80.0d0 0.0d0
0.0d0 0.0d0 80.0d0
pmvol
0.1d0
pmvlpr
1.0d0
rmvol
0.1d0
tavol
0.5d0
pm1boxcbswap
0.20d0
pm1cbswmt
0.14d0 0.28d0 0.42d0 0.56d0 0.70d0 0.84d0 1.0d0
pmcb
0.470d0
pmcbmt
0.0d0 0.16d0 0.32d0 0.49d0 0.66d0 0.83d0 1.0d0
pmall
0.0d0 0.16d0 0.32d0 0.49d0 0.66d0 0.83d0 0.99d0
pmtracm
0.735d0
pmtcmt
0.14d0 0.28d0 0.42d0 0.56d0 0.70d0 0.84d0 1.0d0
rmtrac
0.5d0 0.5d0 0.5d0 0.5d0 0.5d0 0.5d0 0.5d0
tatrac
0.5d0
pmrotate
1.0d0
pmromt
0.0d0 0.16d0 0.32d0 0.49d0 0.66d0 0.83d0 1.0d0
rmrot
0.05d0 0.10d0 0.15d0 0.15d0 0.15d0 0.30d0 0.30d0
tarot
0.5d0
cbmc_formulation
'Martin and Frischknecht 2006'
cbmc_setting_style
'widom ideal'
-----Original Message-----
From: "Thaer Al-Jadir"<tha...@po...>
To: "tow...@li..."<tow...@li...>; "백승환"<kar...@na...>;
Cc:
Sent: 2017-02-06 (월) 05:19:27
Subject: Re: [Towhee-users] Chemical potential calculation with multicomponents
Dear Seunghwan Baek,
I prefer to see your files ( input and force fields) to be more accurate in my answer.
I believe there is a mistake in your force field files. I would suggest you to check it.
Best regards
Thaer Al-Jadir
PhD Student and Teaching assistant at the School of Chemical Engineering and Analytical Science | The University of Manchester | The Mill (B9) | Oxford Road | Manchester | M13 9PL | Tel: 07473889191
________________________________
From: 백승환 <kar...@na...>
Sent: 04 February 2017 03:34:29
To: tow...@li...
Subject: [Towhee-users] Chemical potential calculation with multicomponents
Dear all,
Hello, I am trying to calculate chemical potential for multi-component molecules.
I ran NPT for 10,000 cyles with 7 components having methane, ethane, propane, butane, pentane, hexane, and dodecane.
The results are,
u (Gibbs Total) K 1 1 -4205.520 11.451
u (Gibbs Total) K 2 1 -5189.762 40.365
u (Gibbs Total) K 3 1 -4799.743 76.045
u (Gibbs Total) K 4 1 -3745.663 196.951
u (Gibbs Total) K 5 1 -2728.364 480.996
u (Gibbs Total) K 6 1 -1632.444 214.713
u (Gibbs Total) K 7 1 6518.731 622.668
First, what does the positive value of the chemical potential mean? As far as I know, the chemical potential is negative.
Shown in the manual,
μtotal(i) = μresidual(i) + μdensity(i) + μisolation(i)
μresidual(i) = μNpT Insertion(i) - μIsolation(i).
Since there is no isolation, only μNpT Insertion(i) +μdensity(i) needs to be considered.
μtotal(i) = - kB T ln[ < W * V / ( [N(i)+1] * Λ3(i) ) > ]
μdensity(i) = - kB T ln[ < V / N(i) > / Λ3(i)) ]
μNpT Insertion(i) = - kB T ln[ < V W > / < V > ]
Secondly, I do not understand the following,
μtotal(i) = μdensity(i) + μNpT Insertiona(i)
- kB T ln[ < W * V / ( [N(i)+1] * Λ3(i) ) > ] = - kB T ln[ < V / N(i) > / Λ3(i)) ] - kB T ln[ < V W > / < V > ] = - kB T ln[< V / N(i) > / Λ3(i))*< V W > / < V >]
<=> < W * V / ( [N(i)+1] * Λ3(i) ) > = < V / N(i) > / Λ3(i))*< V W > / < V >
According to Martin and Siepmann 1998 (TCA)<http://towhee.sourceforge.net/references.html#martin_siepmann_1998_tca>.
The term W is <W+>/Wideal where W+ ‡and Wideal are the Rosenbluth weights of the ghost chain and of an ideal chain.
Is this the weighted average insertion probability in Molecular Physics, 1990, 70, 6, 1145-1158, which is equation 6 in page 1150?
Otherwise, how can I calculate this? Which source file I should refer to related to this?
I see, as the number of carbon (length of the molecules) increases, the value of u (NpT Insertion) also increases.
For example,
u (Density) K 6 -5886.576
u (NVT Insertion) K 6 4189.927
u (NpT Insertion) K 6 4189.927
u (Den. + NVT Insert) K 6 -1696.649
u (Den. + NpT Insert) K 6 -1696.649
u (Gibbs Total) K 6 -1698.935
u (Density) K 7 -5523.402
u (NVT Insertion) K 7 11449.852
u (NpT Insertion) K 7 11449.852
u (Den. + NVT Insert) K 7 5926.450
u (Den. + NpT Insert) K 7 5926.450
u (Gibbs Total) K 7 5419.709
I simply assume that the positive value of chemical potential of component-7 comes from this large u (NpT Insertion).
μNpT Insertion(i) = - kB T ln[ < V W > / < V > ]
ln[ < V W > / < V > ] < 0 to get positive μNpT Insertion(i)
then,
[ < V W > / < V > ] < 1
In conclusion, the longer molecules may have smaller W. So I need additional explanation of this W, please.
Moreover, the chemical potential deviation of my simulation is large. Give me suggestion for this and normally, how small they should be?
I would appreciate your help!
*A few days ago, I emailed with similar question as a non-member. You are able not to post the email from this email address. Sorry for that.
Seunghwan Baek
[https://mail.naver.com/readReceipt/notify/?img=hw%2BCaB%2BZM6ndMq2YarkopAtwaAkCM6pCMxCop43oMqMZM4J4F4tqK4ElKoCgMX%2B0MoUl74lR74lcWNFlbX30WLloWrdQaX3cM6kZ74Jn76GCpz0ZtHITbX3Nb4Jv749CW4FcpBFdpBU5M6K5%2B6n%3D.gif]
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From: 백승환 <kar...@na...> - 2017-02-10 16:46:48
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Dear Dr.Martin and all, I checked the chemical potential with several single component in bulk from hexane to octane. Hexane has the negative value of chemical potential and others have positive. In addition, one of example which is Gibbs_Ensemble/Catlow_Zeolite_4a was tested without any modification except the following. nstep 10000 printfreq 1000 blocksize 2000 moviefreq 2000 backupfreq 2000 pdb_output_freq 2000 pressure_virial_freq 20 trmaxdispfreq 20 volmaxdispfreq 20 I ran two times of this and the part of the result is, -----block averages ------Box: 1Block Energy Density Virial Press. Mol fracs 1 -.25026693E+09 0.15432698E+01 0.00000000E+00 0.00956159 0.91791308 0.07252532 2 -.25027411E+09 0.15434928E+01 0.00000000E+00 0.00955056 0.91685404 0.07359539 3 -.25026832E+09 0.15431347E+01 0.00000000E+00 0.00956881 0.91860533 0.07182586 4 -.25026236E+09 0.15431558E+01 0.00000000E+00 0.00956842 0.91856844 0.07186314 5 -.25026588E+09 0.15431771E+01 0.00000000E+00 0.00956669 0.91840245 0.07203085Box: 2Block Energy Density Virial Press. Mol fracs 1 0.26058964E+06 0.61469957E-03 0.96107534E+02 0.00000000 0.00000000 1.00000000 2 0.26021401E+06 0.60954490E-03 0.94329221E+02 0.00000000 0.00000000 1.00000000 3 0.26077062E+06 0.61387740E-03 0.94465403E+02 0.00000000 0.00000000 1.00000000 4 0.25989818E+06 0.61263514E-03 0.96334977E+02 0.00000000 0.00000000 1.00000000 5 0.25971836E+06 0.61219609E-03 0.95164311E+02 0.00000000 0.00000000 1.00000000Please see towhee_citations for a list of suggested citations for this simulation Block Averages ( 5 blocks) Units Type Box Average Standard Deviation u (Gibbs Total) K 3 1 5562.656 146.714u (Gibbs Total) K 3 2 5194.417 34.617u (NpT Insertion) K 3 1 9075.526 152.225u (NpT Insertion) K 3 2 9640.572 34.040u (NVT Insertion) K 3 1 9075.526 152.225u (NVT Insertion) K 3 2 9640.975 33.109 I wonder the meaning of the positive chemical potential, whether is an error or not.According to Theor Chem Acc 1998 99:347-350, The chemical potential of heptane was all negative around -6000 K. Due to this, I guess mine has errors. Any help would be appreciated. Best regards, Seunghwan Baek |
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From: 백승환 <kar...@na...> - 2017-02-07 16:11:57
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Thank you for the email, Al-Jadir,
I do not know there is a mistake in a force field. The "towhee_ff_TraPPE-UA" is what I have used.
I did not change anything in the file, of course.
Even when I tried with only n-dodencae, it resulted in the positive value of chemical potential.
I attahced a part of my input file below.
I would appreciate any comments for this.
Best regards,
inputformat
'Towhee'
ensemble
'npt'
temperature
353.0d0
pressure
3447.38d0
nmolty
7
nmolectyp
502 96 54 30 19 13 92
numboxes
1
stepstyle
'cycles'
nstep
20000
printfreq
2000
blocksize
4000
moviefreq
4000
backupfreq
4000
runoutput
'full'
pdb_output_freq
4000
pressure_virial_freq
10
trmaxdispfreq
40
volmaxdispfreq
40
chempotperstep
10 20 30 40 50 60 120
potentialstyle
'internal'
ffnumber
1
ff_filename
/location/towhee-7.2.0/ForceFields/towhee_ff_TraPPE-UA
classical_potential
'Lennard-Jones'
classical_mixrule
'Lorentz-Berthelot'
lshift
.false.
ltailc
.true.
rmin
1.0d0
rcut
13.8d0
rcutin
10.0d0
electrostatic_form
'none'
linit
F
initboxtype
'dimensions'
initstyle
'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc'
initlattice
'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic'
initmol
502 96 54 30 19 13 92
inix iniy iniz
10 10 10
hmatrix
80.0d0 0.0d0 0.0d0
0.0d0 80.0d0 0.0d0
0.0d0 0.0d0 80.0d0
pmvol
0.1d0
pmvlpr
1.0d0
rmvol
0.1d0
tavol
0.5d0
pm1boxcbswap
0.20d0
pm1cbswmt
0.14d0 0.28d0 0.42d0 0.56d0 0.70d0 0.84d0 1.0d0
pmcb
0.470d0
pmcbmt
0.0d0 0.16d0 0.32d0 0.49d0 0.66d0 0.83d0 1.0d0
pmall
0.0d0 0.16d0 0.32d0 0.49d0 0.66d0 0.83d0 0.99d0
pmtracm
0.735d0
pmtcmt
0.14d0 0.28d0 0.42d0 0.56d0 0.70d0 0.84d0 1.0d0
rmtrac
0.5d0 0.5d0 0.5d0 0.5d0 0.5d0 0.5d0 0.5d0
tatrac
0.5d0
pmrotate
1.0d0
pmromt
0.0d0 0.16d0 0.32d0 0.49d0 0.66d0 0.83d0 1.0d0
rmrot
0.05d0 0.10d0 0.15d0 0.15d0 0.15d0 0.30d0 0.30d0
tarot
0.5d0
cbmc_formulation
'Martin and Frischknecht 2006'
cbmc_setting_style
'widom ideal'
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From: Fouad O. <fou...@un...> - 2017-02-06 16:09:23
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Good morning to all, I would like to calculate the μisolation chemical potential in NVT ensemble for a pure fluid (methane) using pcff forcefield at a given pressure , i read the MCCCS TOWHEE (ALGORITHMS: CHEMICAL POTENTIAL) notice saying that we have to put NMOLECTYP=0. l did do that but I got error messages. I would be grateful if any one could help me. Thanks in advance. Fouad OULEBSIR Ph.D student University of Pau South-west of France. |
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From: Thaer Al-J. <tha...@po...> - 2017-02-05 20:52:14
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Dear Seunghwan Baek, I prefer to see your files ( input and force fields) to be more accurate in my answer. I believe there is a mistake in your force field files. I would suggest you to check it. Best regards Thaer Al-Jadir PhD Student and Teaching assistant at the School of Chemical Engineering and Analytical Science | The University of Manchester | The Mill (B9) | Oxford Road | Manchester | M13 9PL | Tel: 07473889191 ________________________________ From: 백승환 <kar...@na...> Sent: 04 February 2017 03:34:29 To: tow...@li... Subject: [Towhee-users] Chemical potential calculation with multicomponents Dear all, Hello, I am trying to calculate chemical potential for multi-component molecules. I ran NPT for 10,000 cyles with 7 components having methane, ethane, propane, butane, pentane, hexane, and dodecane. The results are, u (Gibbs Total) K 1 1 -4205.520 11.451 u (Gibbs Total) K 2 1 -5189.762 40.365 u (Gibbs Total) K 3 1 -4799.743 76.045 u (Gibbs Total) K 4 1 -3745.663 196.951 u (Gibbs Total) K 5 1 -2728.364 480.996 u (Gibbs Total) K 6 1 -1632.444 214.713 u (Gibbs Total) K 7 1 6518.731 622.668 First, what does the positive value of the chemical potential mean? As far as I know, the chemical potential is negative. Shown in the manual, μtotal(i) = μresidual(i) + μdensity(i) + μisolation(i) μresidual(i) = μNpT Insertion(i) - μIsolation(i). Since there is no isolation, only μNpT Insertion(i) +μdensity(i) needs to be considered. μtotal(i) = - kB T ln[ < W * V / ( [N(i)+1] * Λ3(i) ) > ] μdensity(i) = - kB T ln[ < V / N(i) > / Λ3(i)) ] μNpT Insertion(i) = - kB T ln[ < V W > / < V > ] Secondly, I do not understand the following, μtotal(i) = μdensity(i) + μNpT Insertiona(i) - kB T ln[ < W * V / ( [N(i)+1] * Λ3(i) ) > ] = - kB T ln[ < V / N(i) > / Λ3(i)) ] - kB T ln[ < V W > / < V > ] = - kB T ln[< V / N(i) > / Λ3(i))*< V W > / < V >] <=> < W * V / ( [N(i)+1] * Λ3(i) ) > = < V / N(i) > / Λ3(i))*< V W > / < V > According to Martin and Siepmann 1998 (TCA)<http://towhee.sourceforge.net/references.html#martin_siepmann_1998_tca>. The term W is <W+>/Wideal where W+ ‡and Wideal are the Rosenbluth weights of the ghost chain and of an ideal chain. Is this the weighted average insertion probability in Molecular Physics, 1990, 70, 6, 1145-1158, which is equation 6 in page 1150? Otherwise, how can I calculate this? Which source file I should refer to related to this? I see, as the number of carbon (length of the molecules) increases, the value of u (NpT Insertion) also increases. For example, u (Density) K 6 -5886.576 u (NVT Insertion) K 6 4189.927 u (NpT Insertion) K 6 4189.927 u (Den. + NVT Insert) K 6 -1696.649 u (Den. + NpT Insert) K 6 -1696.649 u (Gibbs Total) K 6 -1698.935 u (Density) K 7 -5523.402 u (NVT Insertion) K 7 11449.852 u (NpT Insertion) K 7 11449.852 u (Den. + NVT Insert) K 7 5926.450 u (Den. + NpT Insert) K 7 5926.450 u (Gibbs Total) K 7 5419.709 I simply assume that the positive value of chemical potential of component-7 comes from this large u (NpT Insertion). μNpT Insertion(i) = - kB T ln[ < V W > / < V > ] ln[ < V W > / < V > ] < 0 to get positive μNpT Insertion(i) then, [ < V W > / < V > ] < 1 In conclusion, the longer molecules may have smaller W. So I need additional explanation of this W, please. Moreover, the chemical potential deviation of my simulation is large. Give me suggestion for this and normally, how small they should be? I would appreciate your help! *A few days ago, I emailed with similar question as a non-member. You are able not to post the email from this email address. Sorry for that. Seunghwan Baek [https://mail.naver.com/readReceipt/notify/?img=hPeCaB%2BZM6n9F6MYarkop4MdK6KXFxv9pzivKzEwpAioMxI0pxEXpxbmtzFXp6UwaLl5WLl51zlqDBFdp6d5MreRhoRdWX%2Bcp6ER%2BBF0bNFgWz0q%2BHK5bre9b4F0p4eZprE5W4kd.gif] |
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From: 백승환 <kar...@na...> - 2017-02-04 03:34:40
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Dear all, Hello, I am trying to calculate chemical potential for multi-component molecules. I ran NPT for 10,000 cyles with 7 components having methane, ethane, propane, butane, pentane, hexane, and dodecane. The results are, u (Gibbs Total) K 1 1 -4205.520 11.451 u (Gibbs Total) K 2 1 -5189.762 40.365 u (Gibbs Total) K 3 1 -4799.743 76.045 u (Gibbs Total) K 4 1 -3745.663 196.951 u (Gibbs Total) K 5 1 -2728.364 480.996 u (Gibbs Total) K 6 1 -1632.444 214.713 u (Gibbs Total) K 7 1 6518.731 622.668 First, what does the positive value of the chemical potential mean? As far as I know, the chemical potential is negative. Shown in the manual, μtotal(i) = μresidual(i) + μdensity(i) + μisolation(i)μresidual(i) = μNpT Insertion(i) - μIsolation(i). Since there is no isolation, only μNpT Insertion(i) +μdensity(i) needs to be considered. μtotal(i) = - kB T ln[ < W * V / ( [N(i)+1] * Λ3(i) ) > ] μdensity(i) = - kB T ln[ < V / N(i) > / Λ3(i)) ]μNpT Insertion(i) = - kB T ln[ < V W > / < V > ] Secondly, I do not understand the following,μtotal(i) = μdensity(i) + μNpT Insertiona(i) - kB T ln[ < W * V / ( [N(i)+1] * Λ3(i) ) > ] = - kB T ln[ < V / N(i) > / Λ3(i)) ] - kB T ln[ < V W > / < V > ] = - kB T ln[< V / N(i) > / Λ3(i))*< V W > / < V >] <=> < W * V / ( [N(i)+1] * Λ3(i) ) > = < V / N(i) > / Λ3(i))*< V W > / < V > According to Martin and Siepmann 1998 (TCA).The term W is <W+>/Wideal where W+ and Wideal are the Rosenbluth weights of the ghost chain and of an ideal chain.Is this the weighted average insertion probability in Molecular Physics, 1990, 70, 6, 1145-1158, which is equation 6 in page 1150? Otherwise, how can I calculate this? Which source file I should refer to related to this? I see, as the number of carbon (length of the molecules) increases, the value of u (NpT Insertion) also increases. For example, u (Density) K 6 -5886.576 u (NVT Insertion) K 6 4189.927 u (NpT Insertion) K 6 4189.927 u (Den. + NVT Insert) K 6 -1696.649 u (Den. + NpT Insert) K 6 -1696.649 u (Gibbs Total) K 6 -1698.935 u (Density) K 7 -5523.402 u (NVT Insertion) K 7 11449.852 u (NpT Insertion) K 7 11449.852 u (Den. + NVT Insert) K 7 5926.450 u (Den. + NpT Insert) K 7 5926.450 u (Gibbs Total) K 7 5419.709 I simply assume that the positive value of chemical potential of component-7 comes from this large u (NpT Insertion). μNpT Insertion(i) = - kB T ln[ < V W > / < V > ]ln[ < V W > / < V > ] < 0 to get positive μNpT Insertion(i) then, [ < V W > / < V > ] < 1 In conclusion, the longer molecules may have smaller W. So I need additional explanation of this W, please.Moreover, the chemical potential deviation of my simulation is large. Give me suggestion for this and normally, how small they should be? I would appreciate your help! *A few days ago, I emailed with similar question as a non-member. You are able not to post the email from this email address. Sorry for that. Seunghwan Baek |
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From: Kaihang S. <ks...@nc...> - 2016-09-04 04:13:13
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Dear Towhee users and developers, Recently I am modifying Towhee code for Ewald Sum in slab geometry. The only thing I have to do is to add a slab correction term, J = 2*pi/V*(∑q_i*z_i)^2, to the total coulombic energy, accounting for the contribution from image cells in z direction. pi is 3.14, V is volume of box, q_i and z_i are the charge and z-coordinate of atom i. I added three additional subroutines to account for this correction term, in energy_change.F file: twh_ec_slab: calculate energy change in slab correction term for chains in chainlist twh_ec_atomlist_slab: calculate energy change in slab correction term for atoms in atomlist in energy.F file: twh_ewald_slab: calculate the energy of slab correction term Accordingly, I've modified subroutines 'twh_engtotal' and 'twh_eng_print' in engtotal.F to include this slab correction term. I've also added this correction term in subroutines 'twh_energy_change' and 'twh_ec_atomlist_nonbond' in energy_change.F to account for the energy change with this slab correction term. I am testing my modified code right now, but some preliminary results are not good. So I was wondering if the modification I've done in Towhee is enough? I want this work for uvt ensemble and I was thinking if I forgot to change the corresponding codes in swap move part. Could any experienced users provide me with some guide on modifying code to serve my purpose? Any comment and advice will be appreciated. Thanks! Best regards, Kaihang |
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From: Marcus M. <mar...@us...> - 2016-08-25 18:18:50
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Howdy Towhee users, Version 7.2.0 of Towhee is now available. Unusually, some of the new variables in towhee_input do not currently do anything useful. I have been rebuilding the volume move routines in order to implement a periodic determination of the pressure via a ghost volume move, but this resulted in a surprising amount of changes being required throughout the code. Normally I would not release a version with knowingly unfinished features, but there have been numerous other bug fixes during this process that justify an early release. A lot of work was done on the configurational-bias routines with particular emphasis on cyclic molecules. Some problems with the MMFF94 force field implementation were resolved, and some issues with CBMC for cyclic molecules using class-2 force fields were also fixed. Marcus -- Marcus G. Martin 88 Martinez Road Edgewood NM 87015-8222 land (505) 286 4457 cell (505) 363 3179 www.photobirder.com towhee.sourceforge.net |
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From: Marcus M. <mar...@us...> - 2016-08-24 18:02:47
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From: HAdi Mokarizadeh <had...@ya...> To: "tow...@li..." <tow...@li... > Cc: Date: Mon, 22 Aug 2016 12:55:02 +0000 (UTC) Subject: Error not a true bonded graph molecule Dear Towhee users I want to use NVT MC simulation for water molcules in zeolite. N_H2O=240 and T=298.0 Kelvin. In the input, type 2 is the H2O and type 1 is zeolite. when I run the input, I get the following error: "Molecule type 2 is not a true bonded graph molecule and has a nonzero move probability of 0.6700000000 for the com translation move". Could you please tell how i can solve this problem? and why this happens? I attached my files ---- The problem comes with how you have set up the input file for the water portion of your simulation. You did it as if all of the waters formed some gigantic super-water molecule that is not bonded together properly. You instead want to have a water molecule that is just the first 3 units of that description. Towhee uses that template for all 240 water molecules, you don't list them all together. Marcus -- Marcus G. Martin 88 Martinez Road Edgewood NM 87015-8222 land (505) 286 4457 cell (505) 363 3179 www.photobirder.com towhee.sourceforge.net |
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From: HAdi M. <had...@ya...> - 2016-08-22 12:55:10
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Dear Towhee users I want to use NVT MC simulation for water molcules in zeolite. N_H2O=240 and T=298.0 Kelvin. In the input, type 2 is the H2O and type 1 is zeolite. when I run the input, I get the following error:"Molecule type 2 is not a true bonded graph molecule and has a nonzero move probability of 0.6700000000 for the com translation move". Could you please tell how i can solve this problem? and why this happens?I attached my filesSincerelyHadi MokarizadehUniversity of Tehran |
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From: HAdi M. <had...@ya...> - 2016-08-12 17:35:16
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Dear Towhee users I want to use NVT MC simulation for water molcules in zeolite. N_H2O=240 and T=298.0 Kelvin. In the input, type 2 is the H2O and type 1 is zeolite. when I run the input, I get the following error:"Molecule type 2 is not a true bonded graph molecule and has a nonzero move probability of 0.6700000000 for the com translation move". Could you please tell how i can solve this problem? and why this happens?I attached my filesSincerelyHadi MokarizadehUniversity of Tehran |
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From: Marcus M. <mar...@us...> - 2016-08-04 19:06:15
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On Mon, Aug 1, 2016 at 1:40 PM, Shenli Zhang <shl...@uc...> wrote: > Dear Towhee users, > > I use Towhee 7.1.0 version to study a yttria stabilized zirconia system > with 5416 atoms in total, and I wrote a script to do MC swap between > yttrium and zirconium, volume change and atom displacement under NPT > condition (P=100 kPa and T=1500). The interaction energy includes short > range exponential-6 form and Coulomb interaction. I set the update of > volume and pressure calculation to be 100, with output frequency =10^5 > (total 10^7). However, I run for 1 day and a half and no block average > comes out. > > I'm quite uncertain if this is a normal speed? I'm also wondering if > anything goes on our cluster could make the calculation slow. > Answering that question depends on many details, but I think it is quite possible that this is a normal result. If you are doing the typical Monte Carlo cycles approach then 10^5 = 100,000 cycles is a pretty long simulation before an output and 10,000,000 cycles is very long. I would generally caution against going to such long simulations right from the start of a new project. The combination of time to equilibrate, and time to fix any human errors in the setup of the move probabilities and so forth means I like to perform many small simulations restarting from the previous output when I'm looking at a new system. Then you will also have a better feel for the time involved in a large production length simulation. Marcus -- Marcus G. Martin 88 Martinez Road Edgewood NM 87015-8222 land (505) 286 4457 cell (505) 363 3179 www.photobirder.com towhee.sourceforge.net |
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From: Shenli Z. <shl...@uc...> - 2016-08-01 20:51:18
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Dear Towhee users, I use Towhee 7.1.0 version to study a yttria stabilized zirconia system with 5416 atoms in total, and I wrote a script to do MC swap between yttrium and zirconium, volume change and atom displacement under NPT condition (P=100 kPa and T=1500). The interaction energy includes short range exponential-6 form and Coulomb interaction. I set the update of volume and pressure calculation to be 100, with output frequency =10^5 (total 10^7). However, I run for 1 day and a half and no block average comes out. I'm quite uncertain if this is a normal speed? I'm also wondering if anything goes on our cluster could make the calculation slow. Thank you so much for your suggestions! Regards, Shenli |
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From: Shenli Z. <shl...@uc...> - 2016-08-01 19:41:03
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Dear Towhee users, I use Towhee 7.1.0 version to study a yttria stabilized zirconia system with 5416 atoms in total, and I wrote a script to do MC swap between yttrium and zirconium, volume change and atom displacement under NPT condition (P=100 kPa and T=1500). The interaction energy includes short range exponential-6 form and Coulomb interaction. I set the update of volume and pressure calculation to be 100, with output frequency =10^5 (total 10^7). However, I run for 1 day and a half and no block average comes out. I'm quite uncertain if this is a normal speed? I'm also wondering if anything goes on our cluster could make the calculation slow. Thank you so much for your suggestions! Regards, Shenli |
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From: Thaer Al-J. <tha...@po...> - 2016-07-16 00:35:44
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Hello, I saw your input file and the chemical potential for water (#-6423.985d0 #-4226.760d0 -5000.0d0) , I don't know which one is the chemical potential for water?. If you want to calculate the density at constant chemical potential then you should enter one value of chemical potential. Yes, average of specific density is the average overall steps . Is your system got equilibration? if not then it need to restart it. Please, read and follow the steps as it written here. Good luck. http://towhee.sourceforge.net/input/towhee_input_v7_0_x.html MCCCS Towhee (towhee_input Version 7.0.x) - SourceForge<http://towhee.sourceforge.net/input/towhee_input_v7_0_x.html> towhee.sourceforge.net Overview. This section covers the variables that are set in the towhee_input file Version 7.0.x. Each variable is listed along with its type (logical, character ... Best regards Thaer Al-Jadir PhD Student and Teaching assistant at the School of Chemical Engineering and Analytical Science | The University of Manchester | The Mill (B9) | Oxford Road | Manchester | M13 9PL | Tel: 07473889191 ________________________________ From: Jungho Yang <ps....@gm...> Sent: 15 July 2016 00:41:21 To: tow...@li... Subject: [Towhee-users] Calculate density Hi all, I am new to Towhee. I want to have chemical potential vs density using GCMC. My system is pure water (TIP3P) at 300 K. In this ensemble, I could calculate density at a constant mu. But I am not sure which density I should use. After simulation, there are averages and one of them is specific density. Is the specific density averaged over all steps or after converged? And Gibbs total chemical potential is not equal to the input chemical potential (-5000). Why? I have also attached the final result and input. Kinds, Jay Averages Units Type Box 1 Volume nm^3 0.80000E+01 Volume^2 nm^6 0.64000E+02 Molecule Number 1 272.121 Molar Volume ml/mol 0.17704E+02 Specific Density g/ml 1.01755331 Number Density nm-3 1 34.01510 Mole Fraction 1 0.9999960 Radius of Gyration A 1 0.3134096 Virial Pressure kPa 0.30299E+06 Virial S_xx kPa 0.31080E+06 Virial S_yy kPa 0.32080E+06 Virial S_zz kPa 0.33790E+06 Virial S_xy kPa 0.20097E+06 Virial S_xz kPa 0.17487E+06 Virial S_yz kPa 0.20679E+06 Virial P_tail kPa -.20174E+05 Virial p_i <x_i><p_v> kPa 1 0.30299E+06 Ideal Pressure kPa 0.18791E+06 Ideal p_i <N/V>kT kPa 1 0.18791E+06 Total Classical K -0.1158E+07 Inter vdw K 0.1697E+06 Angle K 0.0000E+00 Torsion K 0.0000E+00 Intra vdw K 0.0000E+00 External Field K 0.0000E+00 Vibration K 0.0000E+00 Coulomb K -0.1327E+07 Tail vdw K -0.5844E+04 Solvation K 0.0000E+00 u (Density) K 1 -3250.218 u (NVT Insertion) K 1 -1563.311 u (NpT Insertion) K 1 -1563.311 u (Den. + NVT Insert) K 1 -4813.528 u (Den. + NpT Insert) K 1 -4813.528 u (Gibbs Total) K 1 -4871.754 G: Sum{<u_i><N_i>} kJ/mol -0.1102E+05 U kJ/mol -0.9624E+04 pV: <p><V> kJ/mol 0.1459E+04 H: <U> + <p><V> kJ/mol -0.8165E+04 H: <U + pV> kJ/mol -0.8170E+04 S: (<H> - <G>)/T kJ/K mol 0.7142E+01 Z: <p><V>/<N>RT 1.612435 |
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From: Jungho Y. <ps....@gm...> - 2016-07-14 23:41:29
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Hi all,
I am new to Towhee. I want to have chemical potential vs density using GCMC.
My system is pure water (TIP3P) at 300 K. In this ensemble, I could
calculate density at a constant mu. But I am not sure which density I
should use.
After simulation, there are averages and one of them is specific density.
Is the specific density averaged over all steps or after converged?
And Gibbs total chemical potential is not equal to the input chemical
potential (-5000). Why?
I have also attached the final result and input.
Kinds,
Jay
Averages Units Type Box 1
Volume nm^3 0.80000E+01
Volume^2 nm^6 0.64000E+02
Molecule Number 1 272.121
Molar Volume ml/mol 0.17704E+02
Specific Density g/ml 1.01755331
Number Density nm-3 1 34.01510
Mole Fraction 1 0.9999960
Radius of Gyration A 1 0.3134096
Virial Pressure kPa 0.30299E+06
Virial S_xx kPa 0.31080E+06
Virial S_yy kPa 0.32080E+06
Virial S_zz kPa 0.33790E+06
Virial S_xy kPa 0.20097E+06
Virial S_xz kPa 0.17487E+06
Virial S_yz kPa 0.20679E+06
Virial P_tail kPa -.20174E+05
Virial p_i <x_i><p_v> kPa 1 0.30299E+06
Ideal Pressure kPa 0.18791E+06
Ideal p_i <N/V>kT kPa 1 0.18791E+06
Total Classical K -0.1158E+07
Inter vdw K 0.1697E+06
Angle K 0.0000E+00
Torsion K 0.0000E+00
Intra vdw K 0.0000E+00
External Field K 0.0000E+00
Vibration K 0.0000E+00
Coulomb K -0.1327E+07
Tail vdw K -0.5844E+04
Solvation K 0.0000E+00
u (Density) K 1 -3250.218
u (NVT Insertion) K 1 -1563.311
u (NpT Insertion) K 1 -1563.311
u (Den. + NVT Insert) K 1 -4813.528
u (Den. + NpT Insert) K 1 -4813.528
u (Gibbs Total) K 1 -4871.754
G: Sum{<u_i><N_i>} kJ/mol -0.1102E+05
U kJ/mol -0.9624E+04
pV: <p><V> kJ/mol 0.1459E+04
H: <U> + <p><V> kJ/mol -0.8165E+04
H: <U + pV> kJ/mol -0.8170E+04
S: (<H> - <G>)/T kJ/K mol 0.7142E+01
Z: <p><V>/<N>RT 1.612435
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From: Pragati A S. <pa....@nc...> - 2016-03-16 15:54:12
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Dear all, I want to calculate solubility of CO2 in a polymer system. I have used OPLS forcefield for the polymer and prepared an equilibrated system using gromacs. I want to use the same forcefield and system in towhee. But I found out that for the same atomtypes of OPLS, towhee vibcoeff(1) values does not match with the bond constant values of opls in gromacs. For standard harmonic potential, vibcoeff(1) should be equal to "kb" values of gromacs opls ff. But it is not the same. e.g towhee: C CA bond coefficient 0.141900 (should denote bond length) 0.2360085854e+06 ( should denote bond constant, vibcoeff(1)) gromacs opls forcefield i j b kb C CA 0.14900 334720.0 If vibcoeff values in towhee are in kcal/mol and kb values in gromacs are in kj/mol. Still I could not get same values after conversion. ________________________________ Disclaimer: This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.ncl-india.org/files/TermsAndConditions/WebmailDisclamer.aspx |
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From: Shi, J. <sh...@ma...> - 2016-01-30 06:44:09
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Hi there, I got some hint on setting slit pore using hard walls separations from previous postings. However, the thickness of the hard walls increased the volume of the simulation box a lot if the slit pores are very narrow. Since the probability of accepted MC moves will be affected by the box volume, I worry we might get a systematic error here. Thank you in advance for sharing your thoughts. Regards, Jingbo Wood Science department University of British Columbia |
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