exercises:2018_uzh_acpc2:l-j_flu
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exercises:2018_uzh_acpc2:l-j_flu [2018/04/23 12:52] – [Part IV: Ensembles] gtocci | exercises:2018_uzh_acpc2:l-j_flu [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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&MM | &MM | ||
& | & | ||
+ | &SPLINE | ||
+ | | ||
+ | &END | ||
& | & | ||
ATOM Ar # | ATOM Ar # | ||
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& | & | ||
& | & | ||
- | ABC [angstrom] | + | ABC [angstrom] |
| | ||
& | & | ||
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< | < | ||
- | for d in $(seq 2 0.1 4); do | + | for d in $(seq 3.0 0.1 9); do |
sed -e "s|4 0 0|${d} 0 0|" argon.inp > energy_${d}A.inp | sed -e "s|4 0 0|${d} 0 0|" argon.inp > energy_${d}A.inp | ||
cp2k.sopt -i energy_${d}A.inp -o energy_${d}A.out | cp2k.sopt -i energy_${d}A.inp -o energy_${d}A.out | ||
- | awk '/ | + | awk '/ |
done | done | ||
</ | </ | ||
- | * The command '' | + | * The command '' |
- | * With '' | + | * With '' |
- | * '' | + | * '' |
- | * ... and using ''> | + | * ... and using ''> |
* Then we run '' | * Then we run '' | ||
* Using '' | * Using '' | ||
+ | * The energy as a function of distance for all the single point calculations is then printed to the file '' | ||
Plot distance vs. potential energy and find the minimum in energy, which corresponds to the equilibrium distance. After having done it, you can calculate the minimum analytically as well. | Plot distance vs. potential energy and find the minimum in energy, which corresponds to the equilibrium distance. After having done it, you can calculate the minimum analytically as well. | ||
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[[ https:// | [[ https:// | ||
</ | </ | ||
- | ===== Part III: Radial distribution functions | + | ===== Part III: Radial distribution functions |
+ | |||
+ | In this exercise you are asked to compute the radial distribution function of liquid Ar at different temperatures. First of all perform two simulations at 85 K and 150 K for liquid Ar in the NVT ensemble to ensure the simulations are equilibrated at the right temperatures. To perform simulations in NVT copy the relevant section in the input file as shown below. | ||
+ | |||
+ | < | ||
+ | &MD | ||
+ | ENSEMBLE NVT | ||
+ | STEPS 10000 | ||
+ | TIMESTEP 5 | ||
+ | TEMPERATURE 85.0 | ||
+ | & | ||
+ | & | ||
+ | TIMECON 100 # | ||
+ | &END NOSE | ||
+ | &END | ||
+ | &END MD | ||
+ | </ | ||
Use VMD or write your own program (Fortran, C, C++, Python etc.) to calculate radial distribution $g(r)$. Plot $g(r)$, and against various the temperatures to examine the effects. | Use VMD or write your own program (Fortran, C, C++, Python etc.) to calculate radial distribution $g(r)$. Plot $g(r)$, and against various the temperatures to examine the effects. | ||
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===== Part IV: Ensembles | ===== Part IV: Ensembles | ||
- | In previous section, you have already run NVE ensemble molecular dynamics for Ar liquid. In this section, we will focus on the NVT, NPT ensembles. | + | In previous section, you have already run NVE and NVT ensemble molecular dynamics for Ar liquid. In this section, we will focus on the NPT ensembles and you will compare the results in different |
- | Step up NVT calculation, | + | Set up NPT calculation, |
- | + | ||
- | + | ||
- | &MD | + | |
- | ENSEMBLE NVT | + | |
- | STEPS 10000 | + | |
- | TIMESTEP 5 | + | |
- | TEMPERATURE 85.0 | + | |
- | & | + | |
- | & | + | |
- | TIMECON 100 # | + | |
- | &END NOSE | + | |
- | &END | + | |
- | &END MD | + | |
- | + | ||
- | + | ||
- | Step up NPT calculation, | + | |
& | & | ||
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< | < | ||
**TASK** | **TASK** | ||
- | *Run calculations in the NVT ensembles | + | *For the calculations in the NVT ensemble |
*It is a common practice to first perform a simulation in NVT and then run an NVE simulation. What is a possible reason for doing this? | *It is a common practice to first perform a simulation in NVT and then run an NVE simulation. What is a possible reason for doing this? | ||
* It is often needed to perform MD simulations in the NPT ensemble. For the case of Argon, it is liquid at 85 K at atmospheric pressure. First perform an NPT simulation at 85 K and atmospheric pressure. Then, based on the phase diagram reported in this [[https:// | * It is often needed to perform MD simulations in the NPT ensemble. For the case of Argon, it is liquid at 85 K at atmospheric pressure. First perform an NPT simulation at 85 K and atmospheric pressure. Then, based on the phase diagram reported in this [[https:// | ||
- | * For these two simulations plot the time evolution of the cell volume as well as the pressure. To print the cell to file you need to add the keyword &CELL in the print section. For the pressure you can use the following command from the terminal '' | + | * For these two simulations plot the time evolution of the cell volume as well as the pressure. To print the cell to file you need to add the keyword &CELL in the print section. For the pressure you can use the following command from the terminal '' |
- | | + | |
& | & |
exercises/2018_uzh_acpc2/l-j_flu.1524487946.txt.gz · Last modified: 2020/08/21 10:15 (external edit)