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From: <usa...@gm...> - 2020-12-23 20:59:09
|
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From: olan r. <win...@gm...> - 2015-06-25 07:36:29
|
Hello i am new user, in program xmd, i want to make crack simulation using xmd in linux13, but i cannot install it, in my computer... please help me thank before Olan |
From: Rifkin, J. A <jon...@uc...> - 2013-12-10 21:23:42
|
Xianggrong - Under LInux, there are a few ways to pause an XMD program and then resume it. With Windows, the only way I'm aware of is to put the WRITE STATE command into your XMD run file. This will save the current state in a file. You can then use the STATE command in a subsequent run file to read the state back in. Under Linux, you can also hit CTRL-C to automatically create a state file that you can then read in with the STATE command, or you can hit CTRL-Z and pause the program; restarting it with the 'fg' command. But I don't think these are available in Windows. - Jon On 2013-12-10, at 3:11 PM, xiang li <lux...@gm...<mailto:lux...@gm...>> wrote: Hey, I am an newbee to XMD, learning it from last month. Now, I am running some examples downloaded. I have a question that when one simulation is running by DOS, whether it is available to stop temporarily and continue after a while. At the same time ,welcome to give me some suggestions and advices on how to learn XMD well and master it quickly. You would be greatly appreciated if you can give me reply. Best regards, Xiangrong On Wed, Dec 11, 2013 at 3:08 AM, xiang li <lux...@gm...<mailto:lux...@gm...>> wrote: I am very sorry to bother you. I know your Email address from Xmd-support Archives<http://sourceforge.net/mailarchive/forum.php?forum_name=xmd-support>.I am an newbee to XMD. Would you please give me some help about XMD learning. Can you tell me how to construct Cu lattice. I want to simulate impact between Cu and Cu. You would be greatly appreciated if you can reply me as soon as possible. Thank you very much! Xiangrong ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk_______________________________________________ Xmd-support mailing list Xmd...@li... https://lists.sourceforge.net/lists/listinfo/xmd-support |
From: xiang li <lux...@gm...> - 2013-12-10 20:11:12
|
Hey, I am an newbee to XMD, learning it from last month. Now, I am running some examples downloaded. I have a question that when one simulation is running by DOS, whether it is available to stop temporarily and continue after a while. At the same time ,welcome to give me some suggestions and advices on how to learn XMD well and master it quickly. You would be greatly appreciated if you can give me reply. Best regards, Xiangrong On Wed, Dec 11, 2013 at 3:08 AM, xiang li <lux...@gm...> wrote: > I am very sorry to bother you. I know your Email address from Xmd-support > Archives<http://sourceforge.net/mailarchive/forum.php?forum_name=xmd-support>.I > am an newbee to XMD. Would you please give me some help about XMD learning. > Can you tell me how to construct Cu lattice. I want to simulate impact > between Cu and Cu. > > You would be greatly appreciated if you can reply me as soon as possible. > Thank you very much! > > Xiangrong > |
From: Jon R. <jon...@uc...> - 2013-10-21 03:27:24
|
Installation from source code on Windows is not simple, but there is a Windows version of xmd-2.5.32, and there is a video on installing and running that version at http://www.youtube.com/watch?v=RprUCoQWPt0 Let me know if you need the latest version, xmd-2.5.38, on Windows 7. If so, I can try to compile it and post it. It will probably take me a week or two to find the time. Let me know. - Jon On 10/20/2013 08:50 PM, ?? wrote: > Dear all > I don't know how to install and open xmd-2.5.38.tar.gz under win 7,I > need someone help me, if someone reply to me, I will appreciate you > very much! > > > > ------------------------------------------------------------------------------ > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk > > > _______________________________________________ > Xmd-support mailing list > Xmd...@li... > https://lists.sourceforge.net/lists/listinfo/xmd-support |
From: 芙蓉 <525...@qq...> - 2013-10-21 00:50:29
|
Dear all I don't know how to install and open xmd-2.5.38.tar.gz under win 7,I need someone help me, if someone reply to me, I will appreciate you very much! |
From: Jon R. <jon...@uc...> - 2013-02-24 22:10:53
|
Hector, I think the problem is in this part of your input select type 1 velocity linear 1 0 0 3.0e4 select type 1 velocity linear 1 0 0 -3.0e4 You use the exact same SELECT statement, 'select type 1', as assign both the positive and negative velocities. You will need to SELECT the two clusters using different criteria. Perhaps the SELECT BOX command is the best way. First select the cluster on the left and give it your positive velocity, and then select the right cluster, giving it the negative velocity. The exact arguments depend on the velocity of the box. If you're still having trouble, feel free to send your file 'relax_opt_Au_Au-Cubo_147_coord' and I'll return you a working input file. - Jon On 02/24/2013 04:44 PM, Hector Barron wrote: > Dear Jon, > > Thanks for your suggestions, but Im still having a problem to collide > the 2 clusters. You are right I want to collide two Au clusters, so I > have changed the coordinate file by one in which I have two Au > clusters, however when the simulation started both particles moves to > the same direction i.e. seems like xmd just see one whole system and > cannot assign a different velocity to each cluster or maybe there is > something different. What I would like to do is to assign a positive > velocity to the cluster on the left and the same but opposite to the > cluster on the right so then they will collide, but I cannot make it. > Here is again the input file that Im using, I will appreciate any > other suggestion. Thanks!!!! > > read au.txt > > box 300 300 300 > surface on x y z > read relax_opt_Au_Au-Cubo_147_coord > > typename 1 au > > select type 1 > mass 196.97 > > select type 1 > mass 196.97 > > dtime 1.5e-15 > > clamp -1 > itemp 300 > > > select type 1 > velocity linear 1 0 0 3.0e4 > > > select type 1 > velocity linear 1 0 0 -3.0e4 > > > write xmol Cubo147_v3_T300_Au.xyz > > esave 100 energy_147_v3_T300_Au.e > > > repeat 100 > > cmd 500 > > write xmol +Cubo147_v3_T300_Au.xyz > write file +Cubo147_v3_T300_Au.out particle > write pdb config-tmp_Cubo147_v3_T300_Au.pdb > write file +Cubo147_v3_T300_Au.dat temp > > end > > > > > -Hector > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > > > _______________________________________________ > Xmd-support mailing list > Xmd...@li... > https://lists.sourceforge.net/lists/listinfo/xmd-support |
From: Hector B. <he...@gm...> - 2013-02-24 21:45:22
|
Dear Jon, Thanks for your suggestions, but Im still having a problem to collide the 2 clusters. You are right I want to collide two Au clusters, so I have changed the coordinate file by one in which I have two Au clusters, however when the simulation started both particles moves to the same direction i.e. seems like xmd just see one whole system and cannot assign a different velocity to each cluster or maybe there is something different. What I would like to do is to assign a positive velocity to the cluster on the left and the same but opposite to the cluster on the right so then they will collide, but I cannot make it. Here is again the input file that Im using, I will appreciate any other suggestion. Thanks!!!! read au.txt box 300 300 300 surface on x y z read relax_opt_Au_Au-Cubo_147_coord typename 1 au select type 1 mass 196.97 select type 1 mass 196.97 dtime 1.5e-15 clamp -1 itemp 300 select type 1 velocity linear 1 0 0 3.0e4 select type 1 velocity linear 1 0 0 -3.0e4 write xmol Cubo147_v3_T300_Au.xyz esave 100 energy_147_v3_T300_Au.e repeat 100 cmd 500 write xmol +Cubo147_v3_T300_Au.xyz write file +Cubo147_v3_T300_Au.out particle write pdb config-tmp_Cubo147_v3_T300_Au.pdb write file +Cubo147_v3_T300_Au.dat temp end -Hector |
From: Jon R. <jon...@uc...> - 2013-02-22 02:56:54
|
The problem is the TYPE command. The atom types are limited by the potential. The energy and force functions which use the potential expect a value of 1, since you are using a Gold potential. But the name of your file named relax_opt_Ag_Au-Cubo_147_coord suggests that perhaps you intend to have two atom types, Gold (Au) and Silver (Ag)? If you intend to have both Au and Ag atoms, then you'll need an appropriate potential. However, maybe you only intend to have Au atoms, and are using type 1 and type 2 to identify different groups of Au atoms? If so, you will need to change the type 2 atoms to type 1 before you perform any energy or force calculations. You can do that with these commands select type 2 type 1 sometime before your command cmd 500 or maybe just add a type 1 command after the second velocity command, like this select type 2 velocity linear 1 0 0 3.0e4 type 1 If that doesn't help let me know. - Jon On 02/21/2013 08:20 PM, Hector Barron wrote: > Hi, > > I am trying to use XMD to simulate a collision between two gold > clusters, but Im having problems to run it since I get an error > message from my output file saying > > > ERROR (em_energy_list): > Type for particle 2 > is out of range [1..1] > > here is the rest of my input file > > read au.txt > > box 300 300 300 > surface on x y z > read relax_opt_Ag_Au-Cubo_147_coord > > typename 1 Au > typename 2 Au > > select type 1 > mass 196.97 > > select type 2 > mass 196.97 > > dtime 1.5e-15 > > clamp -1 > itemp 300 > > > select type 1 > velocity linear 1 0 0 -16429.40 > > > select type 2 > velocity linear 1 0 0 3.0e4 > > > write xmol Cubo147_v3_T300_Au.xyz > > esave 100 energy_147_v3_T300_Au.e > > > repeat 1000 > > cmd 5000 > > write xmol +Cubo147_v3_T300_Au.xyz > write file +Cubo147_v3_T300_Au.out particle > write pdb config-tmp_Cubo147_v3_T300_Au.pdb > write file +Cubo147_v3_T300_Au.dat temp > > end > > > Is there any input file that I can see to check the way you put the > coordinates of your system to collide them. > > Thanks!!! > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > > > _______________________________________________ > Xmd-support mailing list > Xmd...@li... > https://lists.sourceforge.net/lists/listinfo/xmd-support |
From: Hector B. <he...@gm...> - 2013-02-22 01:20:22
|
Hi, I am trying to use XMD to simulate a collision between two gold clusters, but Im having problems to run it since I get an error message from my output file saying ERROR (em_energy_list): Type for particle 2 is out of range [1..1] here is the rest of my input file read au.txt box 300 300 300 surface on x y z read relax_opt_Ag_Au-Cubo_147_coord typename 1 Au typename 2 Au select type 1 mass 196.97 select type 2 mass 196.97 dtime 1.5e-15 clamp -1 itemp 300 select type 1 velocity linear 1 0 0 -16429.40 select type 2 velocity linear 1 0 0 3.0e4 write xmol Cubo147_v3_T300_Au.xyz esave 100 energy_147_v3_T300_Au.e repeat 1000 cmd 5000 write xmol +Cubo147_v3_T300_Au.xyz write file +Cubo147_v3_T300_Au.out particle write pdb config-tmp_Cubo147_v3_T300_Au.pdb write file +Cubo147_v3_T300_Au.dat temp end Is there any input file that I can see to check the way you put the coordinates of your system to collide them. Thanks!!! |
From: Jon R. <jon...@uc...> - 2011-09-30 13:25:33
|
Dear Changqing Wang - While you can use either potential to model graphene, I don't know how accurate they are. - Jon On Fri, 2011-09-30 at 02:41 -0400, 王昶清 wrote: > Dear Jon Rifkin, > I have a question to ask.Whether or not can we use the Tersoff's Carbon-Silicon or Stillinger-Webers Silicon Potential to simulate the graphene? If not, which potential can be used? > We will be very thankful if you give us a help. > Kind Regards, > Changqing Wang |
From: 王. <cq...@li...> - 2011-09-30 08:37:36
|
Dear Jon Rifkin, I have a question to ask.Whether or not can we use the Tersoff's Carbon-Silicon or Stillinger-Webers Silicon Potential to simulate the graphene? If not, which potential can be used? We will be very thankful if you give us a help. Kind Regards, Changqing Wang |
From: Jon R. <jon...@uc...> - 2011-09-02 15:00:04
|
Keonwook - The reference you want is "Dislocation Generation and Crack Propagation in Metals Examined in Molecular Dynamics Simulations", J. A. Rifkin, C. S. Becquart, D. Kim, P. C. Clapp, MRS Symp. Proc. "Computational Methods in Materials Science", Vol 278, Page 173, 1992 I have just added it to the web site and to the NbAL EAM file. Thanks for alerting me to the problem. Are you planning to do a NbAL simulation? - Jon On 08/30/2011 06:01 PM, Keonwook Kang wrote: > Can anybody tell me the references to Al-Nb eam potential posted on > the web, http://xmd.sourceforge.net/eam/uconn/nbal.txt ? Or if there > is no reference, who should I contact to ask about the potential? > > Thank you, Keonwook > -- ============================================================================== # Jon Rifkin # 860-486-5530 # jon...@uc... # Information Technology Services # University of Connecticut |
From: Keonwook K. <kw...@la...> - 2011-08-30 22:02:07
|
Can anybody tell me the references to Al-Nb eam potential posted on the web, http://xmd.sourceforge.net/eam/uconn/nbal.txt ? Or if there is no reference, who should I contact to ask about the potential? Thank you, Keonwook |
From: 郑兴旺 <zhe...@gm...> - 2011-03-21 09:02:27
|
Do you have the potential file of CuZr ? I didnot make the potential file of CuZr .I need you help me .Thank you ! |
From: Jon R. <jon...@uc...> - 2010-06-25 18:38:42
|
Kevin - I'm not current on the state of X development libraries, but I do know that xmkmf ships with both the latest Ubuntu 10.4 and Debian Lenny. If you are using either of those, xmkmf is included in the xutils-dev package. Hope that helps. - Jon On 06/21/2010 11:43 AM, Kevin Crosby wrote: > Currently, xmdview requires xmkmf to build a makefile. xmkmf is no > longer part of the X development libraries. Is there another way to > install xmdview on a newer system without xmkmf? > > Thanks, > > Kevin > > > ------------------------------------------------------------------------------ > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > _______________________________________________ > Xmd-support mailing list > Xmd...@li... > https://lists.sourceforge.net/lists/listinfo/xmd-support |
From: Kevin C. <kc...@ca...> - 2010-06-21 16:07:32
|
Currently, xmdview requires xmkmf to build a makefile. xmkmf is no longer part of the X development libraries. Is there another way to install xmdview on a newer system without xmkmf? Thanks, Kevin |
From: udayagiri s. b. <uda...@gm...> - 2010-05-25 08:48:01
|
Dear all, In the eam table what is the unit of desity term? is it ev/A^3 or ev or something else?. Can somebody tell me that. Because I have to generate eam (johnson-oh) potential for vanadium from the literature, when I did that all my curves are exactly matching with the literature but when I put the potential in table format readable by xmd, it is giving erraneous value for cohesive energy. I am not sure exactly what is going wrong but wanted to make sure all my units are appropriate. -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. |
From: Jon R. <jon...@uc...> - 2010-05-21 02:33:39
|
Dear Changqing Wang I think that while no technique will always give you the new adatom, the the following commands might help. 'Select near' can select atoms near the original adatom, although it will probably include other atoms as well. 'Select plane' can select atoms which lie between two parallel planes. You can position the planes parallel to the surface so that only atom on the surface are included. Good luck. Please let us know how you solve this problem. Thanks. - Jon On 05/20/2010 08:16 PM, 王昶清 wrote: > Dear Jon Rifkin, We are studying exchange mechanism of adatoms with > substrate during diffusion process by XMD. We expect to output the > adatoms' coordinates during the whole diffusion process. We use the > 'select index ' comand. It can only give adatoms'coordinate before > exchange. How to output the coordinate of adatoms exchanged (new > adatoms) ? Kind Regards, Changqing Wang > ------------------------------------------------------------------------------ > > _______________________________________________ Xmd-support mailing > list Xmd...@li... > https://lists.sourceforge.net/lists/listinfo/xmd-support |
From: 王. <cq...@li...> - 2010-05-21 01:07:25
|
Dear Jon Rifkin, We are studying exchange mechanism of adatoms with substrate during diffusion process by XMD. We expect to output the adatoms' coordinates during the whole diffusion process. We use the 'select index ' comand. It can only give adatoms'coordinate before exchange. How to output the coordinate of adatoms exchanged (new adatoms) ? Kind Regards, Changqing Wang |
From: Jon R. <jon...@uc...> - 2010-05-11 14:06:51
|
Alex - Thank you for your bug report. Neither CELL or CELL2 have been throughly tested. CELL was written by me and tested by me and a collaborator on several different simulations. CELL2 was submitted by the user David Read in 2004. I have tested it less than CELL. I recommend that you try CELL2, reseting CELL_MAX as you said, but first try an adiabatic simulation and verify that the energy remains constant within the same range of roundoff error that the default search gives. Also, if you can compare the execution times of CELL version CELL2, I'd be interested in what you find. I would like to fix the problem you found. This error is mysterious - the condition that tripped the "Failed assertion" seems impossible, because the value the that assertion found less than zero is the ratio of two non-negative numbers; the non-negativity condition is enforced by previous statements. One possible explanation is a memory leak. If possible, could you do one (or both) of the following - Rerun your simulation with the -c option, and send me the output. This will produce messages (a lot of messages) in the standard output that can be used to detect memory leaks. - Send me the input to your simulation so I can rerun it here. Also, which version of XMD are you using? Again, thanks for your feedback. - Jon On 05/11/2010 06:23 AM, Alexander Ovsjannikov wrote: > Dear Jon, > We simulate large system (more then 3e5 atoms) and found that “Time > spent on Neighbor Search” is about 50% of total MD time. > > If we use “NSEARCH CELL” option, Neighbor Search made extremely faster > (more them 1e3 times), but in some cases it cause an error not present > without this option. > (INTERNAL ERROR: Failed assertion ((a->ClampTemp[itag]/CurrentTemp)>=0) > in file cdmd.c line 765.) Would you please explain how to avoid this error? > > When we try “NSEARCH CELL2” sometime sees: > INTERNAL ERROR (CalcNeighborPerAtom): Insufficient storage for > particles in cell; increase CELL_MAX. > It displayed at potentials with large cutoff radius, and of course we > may rebuild XMD with increased value of this constant. Is “CELL2” > algorithm work correct with changes value? > > General question: are these algorithms successfully tested and ready for > usages? Or are they still experimental? > > > Best regards! > Alex Ovsyannikov > -- ============================================================================== # Jon Rifkin # 860-486-5530 # jon...@uc... # Information Technology Services # University of Connecticut |
From: Alexander O. <oll...@gm...> - 2010-05-11 10:23:34
|
Dear Jon, We simulate large system (more then 3e5 atoms) and found that “Time spent on Neighbor Search” is about 50% of total MD time. If we use “NSEARCH CELL” option, Neighbor Search made extremely faster (more them 1e3 times), but in some cases it cause an error not present without this option. (INTERNAL ERROR: Failed assertion ((a->ClampTemp[itag]/CurrentTemp)>=0) in file cdmd.c line 765.) Would you please explain how to avoid this error? When we try “NSEARCH CELL2” sometime sees: INTERNAL ERROR (CalcNeighborPerAtom): Insufficient storage for particles in cell; increase CELL_MAX. It displayed at potentials with large cutoff radius, and of course we may rebuild XMD with increased value of this constant. Is “CELL2” algorithm work correct with changes value? General question: are these algorithms successfully tested and ready for usages? Or are they still experimental? Best regards! Alex Ovsyannikov |