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From: Venkat Padmanabhan <venkat.padmanabhan@ya...>  20060718 22:21:24
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Hi Arun, Thanks for the information. But I'm still not clear about this whole stress thingy. Probably I'm not framing my question properly. Here is my situation in a more detailed way. I am more interested in the triangular components of the stress tensor matrix Sxy, Sxz, and Syz. So, What I am actually looking for are these tensor components for the entire system at each time step. Here is the sample data which I want the stress data to look like (desired Output) time step Sxy Sxz Syz (for the entire system) 1 **** **** **** 2 **** **** **** 3 **** **** **** and so on... But here is what LAMMPS data looks like time step 1 atom id atom type Sxy Sxz Syz (each individual atom) 1 1 **** **** **** 2 1 **** **** **** .... and so on...N values time step 2 atom id atom type Sxy Sxz Syz 1 1 **** **** **** 2 1 **** **** **** .... and so on...N values (N is the total number of atoms in the system. LAMMPS outputs the individual tensor components at every time step. My question is how do I convert them to look like the above desired result. I do not want the tensor components of all the individual atoms. Instead, I want the total value of each component for the system. This is what I did SXY = Sigma (Sxy) ............ added up the contributions of all the atoms SXZ = Sigma (Syz) SYZ = Sigma (Syz) This is not giving me the same result as another software that was used to run a simulation using the same inital configeration. The trajectories match but the stress tensor components do not. I would like to know wether what I did (summation of all the contributions) is the right way to get the stress tensor components for the system or amI missing on something. If not, could you please take some time to help me figure out this. Thank you very much Venkat  Yahoo! Messenger with Voice. Make PCtoPhone Calls to the US (and 30+ countries) for 2¢/min or less. 
From: Arnab Chakrabarty <arnabc@gm...>  20060718 22:58:02

Hi, After summing up the stresses(Sxy Sxz Syz) for all the atoms, a division by system volume(initial or final depending upon the definition of stress ) of the summation is suppose to give Sxy Sxz Syz in actual stress units. You can also use the Pxy Pxz Pyz value obtained from custom thermo command. However in case of Sxy Sxz Syz, the virial contributions of bond, angle etc is not included (refer manual) and so i would prefer Pxy Pxz Pyz. Thanks Arnab Venkat Padmanabhan wrote: > Hi Arun, > Thanks for the information. But I'm still not clear about this whole > stress thingy. Probably I'm not framing my question properly. Here is > my situation in a more detailed way. > > I am more interested in the triangular components of the stress tensor > matrix Sxy, Sxz, and Syz. So, What I am actually looking for are > these tensor components for the entire system at each time step. Here > is the sample data which I want the stress data to look like > > (desired Output) > time step Sxy Sxz Syz (for the entire system) > 1 **** **** **** > 2 **** **** **** > 3 **** **** **** > and so on... > > But here is what LAMMPS data looks like > > time step > 1 > atom id atom type Sxy Sxz Syz (each individual atom) > 1 1 **** **** **** > 2 1 **** **** **** > .... > and so on...N values > time step > 2 > atom id atom type Sxy Sxz Syz > 1 1 **** **** **** > 2 1 **** **** **** > .... > and so on...N values > (N is the total number of atoms in the system. > LAMMPS outputs the individual tensor components at every time step. My > question is how do I convert them to look like the above desired > result. I do not want the tensor components of all the individual > atoms. Instead, I want the total value of each component for the system. > > This is what I did > > SXY = Sigma (Sxy) ............ added up the contributions of all the atoms > SXZ = Sigma (Syz) > SYZ = Sigma (Syz) > > This is not giving me the same result as another software that was > used to run a simulation using the same inital configeration. The > trajectories match but the stress tensor components do not. > > I would like to know wether what I did (summation of all the > contributions) is the right way to get the stress tensor components > for the system or amI missing on something. If not, could you please > take some time to help me figure out this. > Thank you very much > Venkat > >  > Yahoo! Messenger with Voice. Make PCtoPhone Calls > <http://us.rd.yahoo.com/mail_us/taglines/postman1/*http://us.rd.yahoo.com/evt=39663/*http://voice.yahoo.com>; > to the US (and 30+ countries) for 2¢/min or less. > > > > >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys  and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > > >_______________________________________________ >lammpsusers mailing list >lammpsusers@... >https://lists.sourceforge.net/lists/listinfo/lammpsusers > > 
From: Arun Karthi Subramaniyan <asubrama@pu...>  20060719 14:56:43

Venkat, To get the stresses (all 6 components) from the atom stresses this is what you need to do: 1. Sum stress components (Just like what you described) 2. Divide the total stress (from step 1) by the volume of the system Only if you divide the summed stress output you will get the stress in stress units and I think this may be your problem. As Arnab pointed out, the stress tensor in LAMMPS does not include the virial terms from bonds and if you need this included, you should use the pressure tensor instead. Arun Venkat Padmanabhan wrote: > Hi Arun, > Thanks for the information. But I'm still not clear about this whole > stress thingy. Probably I'm not framing my question properly. Here is > my situation in a more detailed way. > =20 > I am more interested in the triangular components of the stress tensor > matrix Sxy, Sxz, and Syz. So, What I am actually looking for are > these tensor components for the entire system at each time step. Here > is the sample data which I want the stress data to look like > =20 > (desired Output) > time step Sxy Sxz Syz (for the entire system) > 1 **** **** **** > 2 **** **** **** > 3 **** **** **** > and so on... > =20 > But here is what LAMMPS data looks like > =20 > time step > 1 > atom id atom type Sxy Sxz Syz (each individual atom) > 1 1 **** **** **** > 2 1 **** **** **** > .... > and so on...N values > time step > 2 > atom id atom type Sxy Sxz Syz > 1 1 **** **** **** > 2 1 **** **** **** > .... > and so on...N values > (N is the total number of atoms in the system. > LAMMPS outputs the individual tensor components at every time step. My > question is how do I convert them to look like the above desired > result. I do not want the tensor components of all the individual > atoms. Instead, I want the total value of each component for the system. > =20 > This is what I did > =20 > SXY =3D Sigma (Sxy) ............ added up the contributions of all the = atoms > SXZ =3D Sigma (Syz) > SYZ =3D Sigma (Syz) > =20 > This is not giving me the same result as another software that was > used to run a simulation using the same inital configeration. The > trajectories match but the stress tensor components do not. > =20 > I would like to know wether what I did (summation of all the > contributions) is the right way to get the stress tensor components > for the system or amI missing on something. If not, could you please > take some time to help me figure out this. > Thank you very much > Venkat > > =  > Yahoo! Messenger with Voice. Make PCtoPhone Calls > <http://us.rd.yahoo.com/mail_us/taglines/postman1/*http://us.rd.yahoo.c= om/evt=3D39663/*http://voice.yahoo.com>; > to the US (and 30+ countries) for 2=A2/min or less. > > > >=  >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share = your >opinions on IT & business topics through brief surveys  and earn cash >http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDEV > > > >_______________________________________________ >lammpsusers mailing list >lammpsusers@... >https://lists.sourceforge.net/lists/listinfo/lammpsusers > =20 > 
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