[SIESTA-L] unable to access inelastic documentation
Dear siesta users I am not being able to open the link http:///sourceforge.net/apps/mediawiki/inelastica in order to get the installation notes and documentationit was working a few days back. Where else can i get the installation notes and documentation? Thanks in advance Regards Akshu
Re: [SIESTA-L] unable to access inelastic documentation
Hi Akshu, For sure, you can download the Inelastica code from the website you mentioned. However in my memory, I never got installation notes and documentation from there when I started the Inelastica package in June. Regarding the installation, you can refer to the following links http://dipc.ehu.es/mediawiki/index.php/Installing_Inelastica_on_URANO http://dipc.ehu.es/mediawiki/index.php/Installing_Inelastica_on_HEMERA I hope that it helps. Cheers! JIn 24/07/2014 4:10 PM, akshu hans wrote: Dear siesta users I am not being able to open the link http:///sourceforge.net/apps/mediawiki/inelastica http:/sourceforge.net/apps/mediawiki/inelastica in order to get the installation notes and documentationit was working a few days back. Where else can i get the installation notes and documentation? Thanks in advance Regards Akshu
[SIESTA-L] convergence test
Dear everyone: I have done the convergence test when I check the convergency (in terms of gradually increase Meshcutoff) of the total energy, I found that the Total energy rise up when I increase the parameter of Meshcutoff (please refer to the accesory) .Is it reasonable? Ahy replay will be appreciated. Dexi Shao converg-1.xls Description: MS-Excel spreadsheet
[SIESTA-L] Huge stress tensor
Dear all, After running just 1 CG step, I got the following stress-tensor-voigt (kbar) Stress-tensot-voigt (kbar) -10092.56 -61.77 5.74 -0.46 0.00 0.00.. My question is can said that the structure is relaxed after the CG step. -- *Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India.* * Ph no-+91-9830512232*
Re: [SIESTA-L] convergence test
Dear Dexi, I wonder what is the unit of your Mesh cutoff? Is it in Ry? Siesta is using atomic orbital as the basis, which is quite different from plane-wave based codes like VASP. In plane-wave code, the plane wave cutoff energy directly determines your basis, and thus influences the result a lot. In Siesta we have the mesh cutoff concept. A large cutoff is required for accurate result. Usually for LDA, 250 Ry is sufficient and for GGA 350 Ry is sufficient. In my opinion you do not need to go up to 600 Ry to check. However, indeed your energy changes too much with Mesh cutoff. Can you upload your input fdf file for more information? Kanhao On Thu, Jul 24, 2014 at 11:43 AM, 邵德喜 dxshao...@gmail.com wrote: Dear everyone: I have done the convergence test when I check the convergency (in terms of gradually increase Meshcutoff) of the total energy, I found that the Total energy rise up when I increase the parameter of Meshcutoff (please refer to the accesory) .Is it reasonable? Ahy replay will be appreciated. Dexi Shao -- Sincerely yours, Kanhao Xue Laboratoire de Réactivité et Chimie des Solides (LRCS) UMR CNRS 7314 Université de Picardie Jules Verne 33 Rue Saint Leu, 80039 Amiens Cedex, France
Re: [SIESTA-L] unable to access inelastic documentation
Dear Akshu, Thanks for making us aware of the broken link to the Inelastica mediawiki page. Apparently SourceForge has simply retired this service very recently. However, I was able to recover the database files etc. and to set up a new mediawiki server here: http://dipc.ehu.es/frederiksen/inelastica/index.php I hope this will work for now. Sincerely, Thomas On 2014-07-24 08:40, akshu hans wrote: Dear siesta users I am not being able to open the link http:///sourceforge.net/apps/mediawiki/inelastica http:/sourceforge.net/apps/mediawiki/inelastica in order to get the installation notes and documentationit was working a few days back. Where else can i get the installation notes and documentation? Thanks in advance Regards Akshu
Re: [SIESTA-L] unable to access inelastic documentation
Hi Thomas, Great! Many thanks! Jin On 24/07/14 20:36, Thomas Frederiksen wrote: Dear Akshu, Thanks for making us aware of the broken link to the Inelastica mediawiki page. Apparently SourceForge has simply retired this service very recently. However, I was able to recover the database files etc. and to set up a new mediawiki server here: http://dipc.ehu.es/frederiksen/inelastica/index.php I hope this will work for now. Sincerely, Thomas On 2014-07-24 08:40, akshu hans wrote: Dear siesta users I am not being able to open the link http:///sourceforge.net/apps/mediawiki/inelastica http:/sourceforge.net/apps/mediawiki/inelastica in order to get the installation notes and documentationit was working a few days back. Where else can i get the installation notes and documentation? Thanks in advance Regards Akshu
Re: [SIESTA-L] unable to access inelastic documentation
Thanks Thomas it is working now. On 24-Jul-2014, at 4:36 pm, Thomas Frederiksen thomas_frederik...@ehu.es wrote: Dear Akshu, Thanks for making us aware of the broken link to the Inelastica mediawiki page. Apparently SourceForge has simply retired this service very recently. However, I was able to recover the database files etc. and to set up a new mediawiki server here: http://dipc.ehu.es/frederiksen/inelastica/index.php I hope this will work for now. Sincerely, Thomas On 2014-07-24 08:40, akshu hans wrote: Dear siesta users I am not being able to open the link http:///sourceforge.net/apps/mediawiki/inelastica http:/sourceforge.net/apps/mediawiki/inelastica in order to get the installation notes and documentationit was working a few days back. Where else can i get the installation notes and documentation? Thanks in advance Regards Akshu
Re: [SIESTA-L] convergence test
Thanks very much.The unit is Ry. I was told that when I get the original structure ,I should do convergence tests first,structual relaxation comes second. In my opinion ,do convergence test without structual relaxation I should set CG step to zero. problem1:I check the convergency (in terms of gradually increase Meshcutoff) of the total energy may be useless because I was told we should check the convergence not of the total energy but of those properties which are relevant for our study in question . But I just want to study the current-voltage relation ,it's expensive for me to check the convergence of its transport property. So I check the convergence of total energy instead opportunisticly. The input.fdf file is as follows. Thans for your replay. Dexi Shao 2014-07-24 18:22 GMT+08:00 Kanhao Xue xuekan...@gmail.com: Dear Dexi, I wonder what is the unit of your Mesh cutoff? Is it in Ry? Siesta is using atomic orbital as the basis, which is quite different from plane-wave based codes like VASP. In plane-wave code, the plane wave cutoff energy directly determines your basis, and thus influences the result a lot. In Siesta we have the mesh cutoff concept. A large cutoff is required for accurate result. Usually for LDA, 250 Ry is sufficient and for GGA 350 Ry is sufficient. In my opinion you do not need to go up to 600 Ry to check. However, indeed your energy changes too much with Mesh cutoff. Can you upload your input fdf file for more information? Kanhao On Thu, Jul 24, 2014 at 11:43 AM, 邵德喜 dxshao...@gmail.com wrote: Dear everyone: I have done the convergence test when I check the convergency (in terms of gradually increase Meshcutoff) of the total energy, I found that the Total energy rise up when I increase the parameter of Meshcutoff (please refer to the accesory) .Is it reasonable? Ahy replay will be appreciated. Dexi Shao -- Sincerely yours, Kanhao Xue Laboratoire de Réactivité et Chimie des Solides (LRCS) UMR CNRS 7314 Université de Picardie Jules Verne 33 Rue Saint Leu, 80039 Amiens Cedex, France
Re: [SIESTA-L] how to get a structure without strain after siesta relaxation
Dear Арсентьев , When I make a strain by decreasing the value of the lattice vector in one direction by the amount of strain, it gives a warning that some atoms are close to each other. Can you tell me how to solve this problem? Regards, Jaret On Tuesday, July 22, 2014 1:02 AM, Jaret Qi jare...@yahoo.com wrote: I have tried the steps you mention to apply a strain but it begins with very high force constraint, i.e. Max 167.125917 constrained which I need it to be less than 0.03 eV/A. Does this sounds ok? Regards, Jaret On Monday, July 21, 2014 8:45 PM, 邵德喜 dxshao...@gmail.com wrote: yes，I have just made a lapse of the pen.I also want to know if strain energy lists anywhere after the calculation in Siesta.Thanks very much. Dexi Shao 2014-07-21 21:20 GMT+08:00 Максим Арсентьев ars21031...@gmail.com: MD.VariableCell false means internal geom. optimization with cell parameters fixed and geom. opt. of internal coordinates of atoms only MD.VariableCell true means full geom. optimization (geom. opt. of both internal coordinates of atoms and cell parameters) so when using MD.VariableCell false cell parameters are fixed 2014-07-21 17:06 GMT+04:00 邵德喜 dxshao...@gmail.com: What do you mean full opt here? And I can not understand full opt. with this option true cell parameters will be the same. In my opnion, cell parameters will be change with MD.VariableCell being false in the structual optimazition. 2014-07-21 20:10 GMT+08:00 Максим Арсентьев ars21031...@gmail.com: When you perform internal optimization with MD.VariableCell false, cell parameters are fixed, so if you further perform full opt. with this option true cell parameters will be the same. So in both these cases cell parameters are the same and you should chose the same kgrig_Monkhorst_Pack block and Briollin zone will not change when you transfer from internal to full geom. optim. 2014-07-21 15:38 GMT+04:00 Kanhao Xue xuekan...@gmail.com: It is strange argument. When the cell parameter changes, the Brillouin zone will change, therefore the Monkhost-Pack K points will change their locations. However, one is just concerned with the rough density of K points in this scheme. Why one cannot use Monkhorst-Pack? On Mon, Jul 21, 2014 at 11:48 AM, 邵德喜 dxshao...@gmail.com wrote: I was told that when MD.VariableCell is setted True, then we can not use block kgrid_Monkhorst_Pack option . Thanks very much . 2014-07-21 15:31 GMT+08:00 Максим Арсентьев ars21031...@gmail.com: You right, you should perform 2 structural relaxations. Before doing this do calculations without geom. optim. with different density of kpoints by %block kgrid_Monkhorst_Pack and see convergence of kpoint density on forces. This also should be checked for meshcutoff - convergence in forces is very important for geom. optim. 2014-07-21 6:59 GMT+04:00 邵德喜 dxshao...@gmail.com: Thanks very much. Do you mean that I should do structual relaxation twice?First with MD.VariableCell False,then with MD.VariableCell True? If I could just do structual relaxation once with MD.VariableCell True? And if kgrid Monkhorst Pack option can be reserved at the same time? Yours Sincerely! Dexishao 2014-07-21 4:55 GMT+08:00 Максим Арсентьев ars21031...@gmail.com: Dear, Dexi! You can vary residual strain by MD.MaxStressTol. Use CG, relax with MD.VariableCell False first, then input coordinates obtained to a new file with MD.VariableCell True. Note you may need to shift some atoms manually before geometry optimization: if all atoms are in 2D plane, then all of them will remain in plane after geom. optim. because z forces are zero, so you need to shift any atom to unlock z forces and avoid such a false state. 2014-07-20 4:01 GMT+04:00 邵德喜 dxshao...@gmail.com: Dear everyone: I really want to know how to get a structure wuthout strain.For example ,Let's consider graphene ,I get the structure from materials studio,and use it as initial one for siesta structual relaxation. If in the relaxation set some options as follows: MD.TypeOfRun CG/Verlet MD.VariableCell True ... At the same time ,I replace kgrid Monkhorst Pack option with k-grid cutoff. When the relaxation is done,I want to ask if the final structure after relaxation is one structure without strain? In general ,how to get a structure without strain is what I care.Thanks in advance. Dexi Shao -- Best wishes, Maxim Arsent'ev, D.Sc.(Chemistry) Laboratory of research of nanostructures Institute of Silicate Chemistry of RAS -- Best wishes, Maxim Arsent'ev, D.Sc.(Chemistry) Laboratory of research of nanostructures Institute of Silicate Chemistry of RAS -- Sincerely yours, Kanhao Xue Laboratoire de Réactivité et Chimie des Solides (LRCS) UMR CNRS 7314 Université de Picardie Jules Verne 33 Rue Saint Leu, 80039 Amiens Cedex, France -- Best wishes, Maxim Arsent'ev, D.Sc.(Chemistry) Laboratory of research of nanostructures
Re: [SIESTA-L] convergence test
I see.You mean that I should set CG steps as usual as we do structual relaxation(foer example :500) during all the convergence tests . And consider kpoint grid convergence first with a reletive high value of Meshcutoff.When it is done ,plot how it depends on FORCES from the output file in the final convergency step .Then consider meshcutoff convergence test with the convergency kpoint grid. When the convergence tests is completed ,structual relaxation is also completed,so I do not need to do structual relaxation additionally. Is it all right? Thanks for all your replay! ( PS: I‘m so sorry but the service is just out of work.I'll upload my input fdf file as soon as it recovers.) Dexi Shao 2014-07-25 1:14 GMT+08:00 Максим Арсентьев ars21031...@gmail.com: Dear Dexi! You should not set nember of CG steps to zero - it is not necessary. You right that you should perform convergence of your property of interest, but first structural relaxation is important as I suppose - maybe not in your case, but often it is so. So select high meshcutoff about 400-500 and vary density of kpoint grid and plot how it depends on FORCES. From this plot you will select kpoints, then take this kpoints fixed and vary meshcutoff to plot dependence on forces again. It is forces, not total energy are relevant for structural relaxation. Enter in google graphene transiesta and 1st link will help I believe. четверг, 24 июля 2014 г. пользователь 邵德喜 написал: Thanks very much.The unit is Ry. I was told that when I get the original structure ,I should do convergence tests first,structual relaxation comes second. In my opinion ,do convergence test without structual relaxation I should set CG step to zero. problem1:I check the convergency (in terms of gradually increase Meshcutoff) of the total energy may be useless because I was told we should check the convergence not of the total energy but of those properties which are relevant for our study in question . But I just want to study the current-voltage relation ,it's expensive for me to check the convergence of its transport property. So I check the convergence of total energy instead opportunisticly. The input.fdf file is as follows. Thans for your replay. Dexi Shao 2014-07-24 18:22 GMT+08:00 Kanhao Xue xuekan...@gmail.com: Dear Dexi, I wonder what is the unit of your Mesh cutoff? Is it in Ry? Siesta is using atomic orbital as the basis, which is quite different from plane-wave based codes like VASP. In plane-wave code, the plane wave cutoff energy directly determines your basis, and thus influences the result a lot. In Siesta we have the mesh cutoff concept. A large cutoff is required for accurate result. Usually for LDA, 250 Ry is sufficient and for GGA 350 Ry is sufficient. In my opinion you do not need to go up to 600 Ry to check. However, indeed your energy changes too much with Mesh cutoff. Can you upload your input fdf file for more information? Kanhao On Thu, Jul 24, 2014 at 11:43 AM, 邵德喜 dxshao...@gmail.com wrote: Dear everyone: I have done the convergence test when I check the convergency (in terms of gradually increase Meshcutoff) of the total energy, I found that the Total energy rise up when I increase the parameter of Meshcutoff (please refer to the accesory) .Is it reasonable? Ahy replay will be appreciated. Dexi Shao -- Sincerely yours, Kanhao Xue Laboratoire de Réactivité et Chimie des Solides (LRCS) UMR CNRS 7314 Université de Picardie Jules Verne 33 Rue Saint Leu, 80039 Amiens Cedex, France -- Best wishes, Maxim Arsent'ev, D.Sc.(Chemistry) Laboratory of research of nanostructures Institute of Silicate Chemistry of RAS
