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From: |
Axel Kohlmeyer <akohlmey@...24...> |

Date: |
Thu, 27 Jul 2017 15:38:38 -0400 |

On Thu, Jul 27, 2017 at 3:31 PM, MASATO KOIZUMI <mkoizumi@...3709...> wrote: > Dear Dr. Axel Kohlmeyer, > > Hello Dr. Kohlmeyer. Thank you for your e-mail. > > I was curious if I could ask a question on an error that I obtained when I > ran my LAMMPS simulation. > > I used a "fix deform" command to change my simulation box such that the > length of the box follows a triangular sinusoidal path using the following > "variable" command. (L0 is the initial box length. Tp is the time period.) > > variable displace equal "v_L0 + (0.5*v_L0)*(1 + > (2/PI)*asin(sin((2*PI*(1/v_Tp)*step*dt) - (PI/2))))" > variable rate equal "(2*v_L0*(1/v_Tp))*(-1)^floor(2*(1/v_Tp)*step*dt)" > fix 4 all deform 1 x variable v_displace v_rate remap v > > > However, I obtained an error statement: ERROR: Power by 0 in variable > formula (../variable.cpp:1718) > > Even when I looked at the LAMMPS error manual, I am not understanding this > error since my variable formula does not have a zero powered to a number. I that is not what the error message says. it says that you have a number raised to the power of 0. axel. > would greatly appreciate if you could inform me a clue in resolving this > error. Thank you. > > Sincerely, > > Masato Koizumi > > On Wed, Jul 19, 2017 at 9:53 AM, Axel Kohlmeyer <akohlmey@...24...> wrote: >> >> On Wed, Jul 19, 2017 at 12:37 PM, MASATO KOIZUMI <mkoizumi@...3709...> >> wrote: >> > Dear Dr. Axel Kohlmeyer, >> > >> > Hello Dr. Kohlmeyer. Thank you for your email. >> > >> > I created a LAMMPS input script that applies tensile and compressive >> > stress >> > on the simulation box that I created using "fix deform" command. >> > >> > I was curious if there is a way to perform cyclic loading without >> > repeating >> > the "fix deform" command. That is, I was curious if there is a way to >> > perform cyclic loading (stretching and compressing) without changing the >> > number of timesteps and the strain rate. Thank you. >> >> please re-read the fix deform command documentation and pay special >> attention to any mentioning of variables. >> >> axel. >> >> > >> > Sincerely, >> > >> > Masato Koizumi >> > >> > On Thu, Jun 8, 2017 at 11:17 AM, Axel Kohlmeyer <akohlmey@...24...> >> > wrote: >> >> >> >> >> >> >> >> On Thu, Jun 8, 2017 at 11:22 AM, MASATO KOIZUMI <mkoizumi@...3709...> >> >> wrote: >> >>> >> >>> Hello All, >> >>> >> >>> This is Masato Koizumi, and I am currently learning how to use LAMMPS. >> >>> >> >>> I was curious if I could ask a question on two commands in LAMMPS: >> >>> special_bonds and pair_style hybrid/overlay. >> >>> >> >>> Observing the LAMMPS manual, I was curious if the command, >> >>> "special_bonds >> >>> lj/coul 0 1 1" means that there are two interactions acting between >> >>> each >> >>> pair of atoms: Lennard-Jones and Coloumb. Lennard-Jones is the >> >>> pairwise >> >>> interaction and Coulomb is the bond interaction. I was curious if the >> >>> 0 1 1 >> >>> means that each pairs of atoms consist either one, two or three bonds. >> >>> 0 >> >>> means that for one-bond pair, the LJ pair potential is turned off. >> >>> Likewise, >> >>> the 1's mean that for two-bond and three-bond pairs, the LJ pair >> >>> potential >> >>> is turned on. >> >> >> >> >> >> this sounds a bit confused, but may be right. you may want to read up >> >> on >> >> what is often called "exclusions" in your preferred MD textbook. >> >> here is my way to describe it: >> >> >> >> if you have a system, where you have non-bonded interactions, e.g. via >> >> pair style lj/cut/coul/cut, *and* bonded interactions e.g. via bond >> >> style >> >> harmonic and angle style harmonic and dihedral style harmonic, then the >> >> special_bonds scaling factors are applied to all 1-2, 1-3, and 1-4 >> >> pairs >> >> connected by bonds. for the default setting (0/0/0), that means when >> >> two >> >> atoms are connected with a bond (i.e. a 1-2 pair), the non-bonded >> >> interaction is turned off, if there are two bonds to the same central >> >> atom >> >> (a-b-c), then the 1-3 interaction (a-c) is scaled by the 1-3 factor. if >> >> there is also a bond between a-c, then the 1-2 factor is applied. same >> >> rules >> >> apply for 1-4 pairs and the 1-4 special bonds factor. >> >> >> >>> >> >>> >> >>> >> >>> Lastly, for pair_style hybrid/overlay, I was curious if this command >> >>> simply means that the potential energy between each pairs of atoms is >> >>> the >> >>> summation of the pair potentials. That is, pair_style hybrid/overlay >> >>> lj/cut >> >>> 2.5 coul/long 2.0 is defined as the summation of Lennard-Jones and >> >>> Coulomb >> >>> potential acting between each pairs of atoms. >> >> >> >> >> >> yes, this would be the same as lj/cut/coul/long 2.5 2.0. please make a >> >> test and see for yourself. >> >> >> >> axel. >> >> >> >> >> >>> >> >>> >> >>> Thank you. >> >>> >> >>> >> >>> Masato >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> ------------------------------------------------------------------------------ >> >>> Check out the vibrant tech community on one of the world's most >> >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> >>> _______________________________________________ >> >>> lammps-users mailing list >> >>> lammps-users@lists.sourceforge.net >> >>> https://lists.sourceforge.net/lists/listinfo/lammps-users >> >>> >> >> >> >> >> >> >> >> -- >> >> Dr. Axel Kohlmeyer akohlmey@...24... http://goo.gl/1wk0 >> >> College of Science & Technology, Temple University, Philadelphia PA, >> >> USA >> >> International Centre for Theoretical Physics, Trieste. Italy. >> > >> > >> >> >> >> -- >> Dr. Axel Kohlmeyer akohlmey@...24... http://goo.gl/1wk0 >> College of Science & Technology, Temple University, Philadelphia PA, USA >> International Centre for Theoretical Physics, Trieste. Italy. > > -- Dr. Axel Kohlmeyer akohlmey@...24... http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.

**Follow-Ups**:**Re: [lammps-users] Inquiry on LAMMPS fix_deform and variable formula"***From:*Axel Kohlmeyer <akohlmey@...24...>

**References**:**Re: [lammps-users] Inquiry on LAMMPS fix_deform and variable formula"***From:*MASATO KOIZUMI <mkoizumi@...3709...>

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