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From: enrique m. <enr...@gm...> - 2023-09-14 12:33:43
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Hello, When following the example for the dynamical_matrix command (here <https://github.com/lammps/lammps/tree/develop/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon>) and turning on the minimization flag, there are substantial negative values. Here are the first six lines of the output file that’s generated when I run it: 5407.73126648 0.60396688 0.00000175 -1276.30761693 -861.92746902 -861.81428983 -193.16889479 0.00650038 -0.00000008 -1276.30761624 -861.92746857 861.81429082 -193.17584859 -0.02457904 0.00000000 -1276.12053965 861.59922389 -861.65460775 This shouldn’t be the case for a minimized configuration, right? Shouldn’t the elements of the Hessian should be positive at a minimum? The matrix’s eigenvalues are negative as well (using this tool <https://github.com/xfanak/lammps-dynamical-matrix/tree/main>). The first 8 are: 8562.748779308313 7914.9129841273425 6797.395660302146 -7513.893638723845 6003.365898566742 -6962.005429797687 -5894.101569206084 -5543.162808769083 I have tried the command on other systems as well, and there have been negative values in every case. I’m not really sure what to make of this. |
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From: Alvaro D. G. <aga...@pu...> - 2020-06-14 22:14:44
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I want to use 2 different bonds represented by two different tables something like bond_style hybrid table linear 120001 table spline 120001 bond_coeff 1 table bondsim31.table bond bond_coeff 2 table bondsim32.table bond But I receive the error style hybrid cannot use same bond style twice does anyone knows how to circumvent this problem |
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From: Jannat A. <jannatahmed2023@u.northwestern.edu> - 2020-04-17 05:10:25
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Hello, I am using the Green -Kubo formulation to calculate thermal conductivity of 2,2 dimethyl butane (a small molecule having 20 atoms). My simulation box contains 250 molecules. I have a concern if I am plotting ACF correctly. The following lammps command is used to calculate the autocorrelation function *fix JJ all ave/correlate 1 4000 4000 c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.dat ave running* J0Jt.dat contains autocorrelation values for every 4 ps time window. I am confused how to plot the autocorrelation function. I know I should plot columns 4,5,6 against column 2 (time delta). But the thing is there is data for many time windows. As there is also an averaging done (ave running), should I plot the last time window? Can anyone please help me figure this out and to understand more. Thanks a lot. Jannat |
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From: Jannat A. <jannatahmed2023@u.northwestern.edu> - 2020-04-17 00:13:12
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Hello, I am using the Green -Kubo formulation to calculate thermal conductivity of 2,2 dimethyl butane (a small molecule having 20 atoms). My simulation box contains 250 molecules. I have a concern if I am plotting ACF correctly. The following lammps command is used to calculate the autocorrelation function *fix JJ all ave/correlate 1 4000 4000 c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.dat ave running* J0Jt.dat contains autocorrelation values for every 4 ps time window. I am confused how to plot the autocorrelation function. I know I should plot columns 4,5,6 against column 2 (time delta). But the thing is there is data for many time windows. As there is also an averaging done (ave running), should I plot the last time window? Can anyone please help me figure this out and to understand more. Thanks a lot. Jannat |
