tag:blogger.com,1999:blog-6172620873343846436.post651230415990105591..comments2024-03-28T02:21:49.239-07:00Comments on NZ Nano: Molecular dynamics in PythonJacob Martinhttp://www.blogger.com/profile/13042491185977653368noreply@blogger.comBlogger17125tag:blogger.com,1999:blog-6172620873343846436.post-82304072138283979722023-01-22T23:18:48.477-08:002023-01-22T23:18:48.477-08:00The velocities and distances are all in reduced un...The velocities and distances are all in reduced units which is scaled to the box size. We are also using reduced mass units. Jacob Martinhttps://www.blogger.com/profile/13042491185977653368noreply@blogger.comtag:blogger.com,1999:blog-6172620873343846436.post-82457572586664622032023-01-17T19:16:57.462-08:002023-01-17T19:16:57.462-08:00Hello, why did you multiply the velocities by the ...Hello, why did you multiply the velocities by the box size? Also, no mass was included in the calculation of kinetic energy, does it have to do with reduced unit?<br /><br />Thank you very muchAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-6172620873343846436.post-50550468780659244062023-01-06T21:00:23.407-08:002023-01-06T21:00:23.407-08:00You need to remove the line importing the data and...You need to remove the line importing the data and include the line pos = np.random.rand(N,DIM)*BoxSizeJacob Martinhttps://www.blogger.com/profile/13042491185977653368noreply@blogger.comtag:blogger.com,1999:blog-6172620873343846436.post-12541852178104503612022-07-15T08:19:50.140-07:002022-07-15T08:19:50.140-07:00This was from the orginal Fortran code and it took...This was from the orginal Fortran code and it took me some time to realise that it is due to the normalised units. So it is really F(r*)=1/r dE/dr* and is required when going from the force equation in the normal units to the reduced units. Jacob Martinhttps://www.blogger.com/profile/13042491185977653368noreply@blogger.comtag:blogger.com,1999:blog-6172620873343846436.post-8328677641128774072022-07-15T07:17:57.804-07:002022-07-15T07:17:57.804-07:00You have defined F in two different ways at two di...You have defined F in two different ways at two different places. 1) F = -dE/dr. 2) F = - 1/r dE/dr.<br />You have used the second one in the code as well. I guess that's wrong. The first definition without an additional 1/r is correct. <br />What do you think?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6172620873343846436.post-41179656449560786802022-06-29T09:11:02.861-07:002022-06-29T09:11:02.861-07:00Hi Jacon,
Great post. Just a question. Why are yo...Hi Jacon,<br /><br />Great post. Just a question. Why are you setting the value of boltzmann constant to 1? Surely that makes T* = T?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6172620873343846436.post-53505240389227890192022-06-29T09:09:19.957-07:002022-06-29T09:09:19.957-07:00Great article. However one question. Why did you s...Great article. However one question. Why did you set the botltzmann constant to 1? surely that makes T* = T right.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6172620873343846436.post-54211708859890046232022-01-07T19:03:22.008-08:002022-01-07T19:03:22.008-08:00This comment has been removed by the author.Jacob Martinhttps://www.blogger.com/profile/13042491185977653368noreply@blogger.comtag:blogger.com,1999:blog-6172620873343846436.post-86626230060122036872022-01-03T07:37:32.893-08:002022-01-03T07:37:32.893-08:00To use the program as it is, I am looking for the ...To use the program as it is, I am looking for the way not to load the ouptut.dat (not existing) but to generate it directly in the code :<br />pos = np.random.rand(DIM, 2)<br />but the boxsize = 10 so we need to *10 ?<br /><br />thanksAnonymoushttps://www.blogger.com/profile/07275818788499485817noreply@blogger.comtag:blogger.com,1999:blog-6172620873343846436.post-4611491222555901422021-01-08T12:34:56.279-08:002021-01-08T12:34:56.279-08:00Hi Jacob,
Thanks for this post. What are you usin...Hi Jacob,<br /><br />Thanks for this post. What are you using for output.dat? Just a random initial configuration or an output from lammps?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6172620873343846436.post-16854069267505116452020-12-17T13:03:42.886-08:002020-12-17T13:03:42.886-08:00Thanks for spotting this. It has been corrected.Thanks for spotting this. It has been corrected.Jacob Martinhttps://www.blogger.com/profile/13042491185977653368noreply@blogger.comtag:blogger.com,1999:blog-6172620873343846436.post-60032565443364929872020-10-31T19:19:40.240-07:002020-10-31T19:19:40.240-07:00No this is incorrect thank you for picking this up...No this is incorrect thank you for picking this up. I copied this straight from the Fortran code this is based on. This has been corrected and the plots redone. Here is a nice write up on computing the pressure using the virial coefficient. http://www.sklogwiki.org/SklogWiki/index.php/PressureJacob Martinhttps://www.blogger.com/profile/13042491185977653368noreply@blogger.comtag:blogger.com,1999:blog-6172620873343846436.post-92046836223650439472020-09-26T06:29:00.685-07:002020-09-26T06:29:00.685-07:00This comment has been removed by the author.Jacob Martinhttps://www.blogger.com/profile/13042491185977653368noreply@blogger.comtag:blogger.com,1999:blog-6172620873343846436.post-36539393670890026562020-09-22T03:31:38.735-07:002020-09-22T03:31:38.735-07:00In the virial calculation force is multiplied by t...In the virial calculation force is multiplied by the square of the distance not the distance itself . Is it correct ?!Anonymoushttps://www.blogger.com/profile/05251640936975337382noreply@blogger.comtag:blogger.com,1999:blog-6172620873343846436.post-15611673093941299352019-12-06T13:47:11.618-08:002019-12-06T13:47:11.618-08:00Very helpful. Thanks!Very helpful. Thanks!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6172620873343846436.post-55254742779560224202019-05-02T23:48:40.370-07:002019-05-02T23:48:40.370-07:00I would edit the output.dat file in a text browser...I would edit the output.dat file in a text browser like notepad++ so that it reads like a normal xyz files then save it with .xyz ending.<br />So with this format it would look like this<br /><br />N_atoms<br /><br />element atom1_x atom2_y atom_z<br /><br />e.g.<br />3<br /><br />O -0.50276 -0.03361 0.00002<br />H 0.30991 -0.56099 -0.02030<br />H -1.21066 -0.69507 0.01772<br /><br />A tip to edit the file quickly is to use the alt key while highlighting to be able to highlight vertically. https://notepad-plus-plus.org/features/column-mode-editing.html<br /><br />Another option is to use OVITO that lets you put in any file and specify which columns are the x, y and z positions.<br /><br />All the best,Jacob Martinhttps://www.blogger.com/profile/13042491185977653368noreply@blogger.comtag:blogger.com,1999:blog-6172620873343846436.post-50878262613064984442019-04-15T08:12:24.720-07:002019-04-15T08:12:24.720-07:00In trying to run your moldyn script in my compute...In trying to run your moldyn script in my computer I am held up by<br />the position file 'output.dat'. Can you tell me how to produce it<br />using the numpy random module for any N ?<br />Thanks in advance<br />Anandaram anandaramhttps://www.blogger.com/profile/02535579989244620135noreply@blogger.com