Liquid Si - Standard MD - Revision history

Singraber at 21:30, 17 October 2025

2025-10-17T21:30:43Z

Karsai: /* Download */

2019-11-14T09:43:55Z

Download

← Older revision		Revision as of 09:43, 14 November 2019
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	== Download ==		== Download ==
	[~~http~~:~~//www.vasp.at/vasp-workshop/examples/~~Si_Liquid_Melting.tgz Si_Liquid_Melting.tgz]		[[Media:Si_Liquid_Melting.tgz\| Si_Liquid_Melting.tgz]]

	{{Template:Molecular dynamics - Tutorial}}		{{Template:Molecular dynamics - Tutorial}}

	[[Category:Examples]]		[[Category:Examples]]

Karsai at 12:00, 1 October 2019

2019-10-01T12:00:49Z

← Older revision		Revision as of 12:00, 1 October 2019
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	At this point the user should be able to monitor the energies in the calculation. If not repeat from scratch!		At this point the user should be able to monitor the energies in the calculation. If not repeat from scratch!

	'''~~User task~~:''' Compare the energy conservation of the microcanonical ensemble and the canonical ensemble. Carry out another 200 molecular dynamics steps but with a step size that is only the half of the previous one ({{TAG\|POTIM}}=1.5). Compare the energy conservation and check the mean temperature!		'''Exercise:''' Compare the energy conservation of the microcanonical ensemble and the canonical ensemble. Carry out another 200 molecular dynamics steps but with a step size that is only the half of the previous one ({{TAG\|POTIM}}=1.5). Compare the energy conservation and check the mean temperature!

	=== Further things to try ===		=== Further things to try ===

Karsai: /* Download */

2019-09-26T10:43:31Z

Download

← Older revision		Revision as of 10:43, 26 September 2019
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	== Download ==		== Download ==
	[http://www.vasp.at/vasp-workshop/examples/~~Si_liquid_melting~~.tgz ~~Si_liquid_melting~~.tgz]		[http://www.vasp.at/vasp-workshop/examples/Si_Liquid_Melting.tgz Si_Liquid_Melting.tgz]

	{{Template:Molecular dynamics - Tutorial}}		{{Template:Molecular dynamics - Tutorial}}

	[[Category:Examples]]		[[Category:Examples]]

Karsai: /* Further things to try */

2019-07-03T15:42:15Z

Further things to try

← Older revision		Revision as of 15:42, 3 July 2019
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	=== Further things to try ===		=== Further things to try ===
	To get a better statistics the user should further carry out the calculation for 400-1000 steps in the {{TAG\|NVT ensemble}} but with a much smaller time step {{TAGBL\|POTIM}}=0.3. Repeat the above analysis!		To get a better statistics the user should further carry out the calculation for 400-1000 steps in the {{TAG\|NVT ensemble}} but with a much smaller time step {{TAGBL\|POTIM}}=0.3. '''Repeat the above analysis!'''

	== Download ==		== Download ==

Karsai: /* Microcanonical ensemble */

2019-07-03T15:41:54Z

Microcanonical ensemble

← Older revision		Revision as of 15:41, 3 July 2019
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	We will carry out two hundred more molecular dynamics steps (by setting {{TAG\|NSW}}=200) using the microcanonical ensemble.		We will carry out two hundred more molecular dynamics steps (by setting {{TAG\|NSW}}=200) using the microcanonical ensemble.

			First we check the mean temperature by typing the following line
			grep "mean temperature" OUTCAR
			The user should get an output like:
			mean temperature <T/S>/<1/S> : 2566.129
			In this example we see that the target temperature is not kept when a microcanonical ensemble is used.

			At this point the user should be able to monitor the energies in the calculation. If not repeat from scratch!

			'''User task:''' Compare the energy conservation of the microcanonical ensemble and the canonical ensemble. Carry out another 200 molecular dynamics steps but with a step size that is only the half of the previous one ({{TAG\|POTIM}}=1.5). Compare the energy conservation and check the mean temperature!

			=== Further things to try ===
			To get a better statistics the user should further carry out the calculation for 400-1000 steps in the {{TAG\|NVT ensemble}} but with a much smaller time step {{TAGBL\|POTIM}}=0.3. Repeat the above analysis!

	== Download ==		== Download ==

Karsai at 15:27, 3 July 2019

2019-07-03T15:27:59Z

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   gnuplot -e "set terminal jpeg; set xlabel 'N_{step}'; set ylabel 'Total energy (eV/cell)';set style data lines; plot 'energy.dat'" > energy_750fs.jpg
 The energy vs number of iteration should look like Fig. 5. We see that after a few 100 fs the energy is conserved, but of course with some fluctuations present. This should also indicate that the structure is not changing drastically anymore and that the melting is achieved. We should note that the energy conservation can be monitored because we use the deterministic {{TAG|Nose-Hoover thermostat}} which has a kinetic and potential energy term of the heat bath which provides energy conservation. If we would use e.g. the {{TAG|Langevin thermostat}} which is a stochastic thermostat we would obtain large fluctuations in the total energy.
 == Download ==

Karsai at 15:35, 2 July 2019

2019-07-02T15:35:07Z

← Older revision		Revision as of 15:35, 2 July 2019
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	grep "free energy" OUTCAR\|awk ' {print $5}' >> energy.dat		grep "free energy" OUTCAR\|awk ' {print $5}' >> energy.dat

	=== Further ~~continuing~~ ===		=== Further continuation ===
	We continue the calculation for 450 fs.		We continue the calculation for 450 fs.
	[[File:PC 750fs.jpg\|300px\|thumb\|Fig. 4: Pair correlation functions after 750, 300 and 150 fs.]]		[[File:PC 750fs.jpg\|300px\|thumb\|Fig. 4: Pair correlation functions after 750, 300 and 150 fs.]]

Karsai at 17:03, 1 July 2019

2019-07-01T17:03:30Z

Karsai: /* 150 fs */

2019-07-01T16:59:53Z

150 fs

← Older revision		Revision as of 16:59, 1 July 2019
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	=== 150 fs ===		=== 150 fs ===
	First we run the calculation for 150 fs.		First we run the calculation for 150 fs.
	[[File:PC ~~150ps~~.jpeg\|300px\|thumb\|Fig. 1: Pair correlation function after 150 fs.]]		[[File:PC 150fs.jpeg\|300px\|thumb\|Fig. 1: Pair correlation function after 150 fs.]]
	[[File:Energy_150ps.jpg\|300px\|thumb\|Fig. 2: Total energy vs number of steps in first 150 fs.]]		[[File:Energy_150ps.jpg\|300px\|thumb\|Fig. 2: Total energy vs number of steps in first 150 fs.]]
	*Pair correlation function:		*Pair correlation function:

← Older revision		Revision as of 21:30, 17 October 2025
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	*To select a molecular dynamics calculation set {{TAG\|IBRION}}=0.		*To select a molecular dynamics calculation set {{TAG\|IBRION}}=0.
	*By selecting {{TAG\|MDALGO}}=2 and {{TAG\|ISIF}}=2 we select the {{TAG\|NVT ensemble}} using the ~~{{TAG\|Nose~~-Hoover thermostat}}.		*By selecting {{TAG\|MDALGO}}=2 and {{TAG\|ISIF}}=2 we select the {{TAG\|NVT ensemble}} using the [[Nosé-Hoover thermostat]].
	*The tag {{TAG\|SMASS}} specifies the ~~Nose~~ mass, which is a ~~ficitional~~ mass for the fictional coordinate of the heat bath. The choice of {{TAGBL\|SMASS}}=1.0 should work well for this tutorial.		*The tag {{TAG\|SMASS}} specifies the Nosé mass, which is a fictitious mass for the fictional coordinate of the heat bath. The choice of {{TAGBL\|SMASS}}=1.0 should work well for this tutorial.
	*Since we are dealing with a super cell, we set {{TAGBL\|LREAL}}=Auto. In this mode the projection operators are evaluated in real space. This should speed up the calculation while being slightly less accurate then the evaluation of the operators in reciprocal space.		*Since we are dealing with a super cell, we set {{TAGBL\|LREAL}}=Auto. In this mode the projection operators are evaluated in real space. This should speed up the calculation while being slightly less accurate then the evaluation of the operators in reciprocal space.
	*To significantly speed up the calculations we use {{TAGBL\|ALGO}}=''VeryFast'' and {{TAGBL\|PREC}}=''Low''. This is ok for this tutorial example but for more precise results these flags should be used with caution!		*To significantly speed up the calculations we use {{TAGBL\|ALGO}}=''VeryFast'' and {{TAGBL\|PREC}}=''Low''. This is ok for this tutorial example but for more precise results these flags should be used with caution!
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	After that we plot the ''energy.dat'' file:		After that we plot the ''energy.dat'' file:
	gnuplot -e "set terminal jpeg; set xlabel 'N_{step}'; set ylabel 'Total energy (eV/cell)';set style data lines; plot 'energy.dat'" > energy_750fs.jpg		gnuplot -e "set terminal jpeg; set xlabel 'N_{step}'; set ylabel 'Total energy (eV/cell)';set style data lines; plot 'energy.dat'" > energy_750fs.jpg
	The energy vs number of iteration should look like Fig. 5. We see that after a few 100 fs the energy is conserved, but of course with some fluctuations present. This should also indicate that the structure is not changing drastically anymore and that the melting is achieved. We should note that the energy conservation can be monitored because we use the deterministic ~~{{TAG\|Nose~~-Hoover thermostat}} which has a kinetic and potential energy term of the heat bath which provides energy conservation. If we would use e.g. the ~~{{TAG\|~~Langevin thermostat}} which is a stochastic thermostat we would obtain large fluctuations in the total energy.		The energy vs number of iteration should look like Fig. 5. We see that after a few 100 fs the energy is conserved, but of course with some fluctuations present. This should also indicate that the structure is not changing drastically anymore and that the melting is achieved. We should note that the energy conservation can be monitored because we use the deterministic [[Nosé-Hoover thermostat]] which has a kinetic and potential energy term of the heat bath which provides energy conservation. If we would use e.g. the [[Langevin thermostat]] which is a stochastic thermostat we would obtain large fluctuations in the total energy.

	=== Microcanonical ensemble ===		=== Microcanonical ensemble ===
	Next we want to continue the calculations but instead of the canonical ensemble (~~{{TAG\|~~NVT ensemble}}) we are going to carry out the calculations in the microcanonical ensemble ({{TAG\|NVE ensemble}}). The microcanonical ensemble calculations are carried out by setting the following tags in the {{TAG\|INCAR}} file:		Next we want to continue the calculations but instead of the canonical ensemble ([[NVT ensemble]]) we are going to carry out the calculations in the microcanonical ensemble ({{TAG\|NVE ensemble}}). The microcanonical ensemble calculations are carried out by setting the following tags in the {{TAG\|INCAR}} file:
	{{TAGBL\|MDALGO}} = 1		{{TAGBL\|MDALGO}} = 1
	{{TAGBL\|ANDERSEN_PROB}} = 0.0		{{TAGBL\|ANDERSEN_PROB}} = 0.0

← Older revision		Revision as of 17:03, 1 July 2019
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	First we run the calculation for 150 fs.		First we run the calculation for 150 fs.
	[[File:PC 150fs.jpeg\|300px\|thumb\|Fig. 1: Pair correlation function after 150 fs.]]		[[File:PC 150fs.jpeg\|300px\|thumb\|Fig. 1: Pair correlation function after 150 fs.]]
	[[File:~~Energy_150ps~~.jpg\|300px\|thumb\|Fig. 2: Total energy vs number of steps in first 150 fs.]]		[[File:Energy_150fs.jpg\|300px\|thumb\|Fig. 2: Total energy vs number of steps in first 150 fs.]]
	*Pair correlation function:		*Pair correlation function:
	The pair correlation function is written out to the {{TAG\|PCDAT}} file. The abscissa of that file is within mesh points of a selected grid and need to be converted to <math>\AA</math>. This is done by invoking the following short awk script on the command line:		The pair correlation function is written out to the {{TAG\|PCDAT}} file. The abscissa of that file is within mesh points of a selected grid and need to be converted to <math>\AA</math>. This is done by invoking the following short awk script on the command line:
	awk <PCDAT >PCDAT.150fs ' NR==8 {pcskal=$1} NR==9 {pcfein=$1} NR>=13 {line=line+1; print (line-0.5)*pcfein/pcskal,$1} '		awk <PCDAT >PCDAT.150fs ' NR==8 {pcskal=$1} NR==9 {pcfein=$1} NR>=13 {line=line+1; print (line-0.5)*pcfein/pcskal,$1} '
	This produces the file PCDAT.~~150ps~~ which contains the pair correlation function against the radius in Angstrom after the first 150 ps (50 timesteps {{TAG\|NSW}}=50 with a stepsize of 3 ps {{TAG\|POTIM}}=3).		This produces the file PCDAT.150fs which contains the pair correlation function against the radius in Angstrom after the first 150 fs (50 timesteps {{TAG\|NSW}}=50 with a stepsize of 3 fs {{TAG\|POTIM}}=3).
	Now we will plot the pair correlation function in the gnuplot window:		Now we will plot the pair correlation function in the gnuplot window:
	gnuplot -e "set xlabel 'r(Ang)'; set ylabel 'PCF'; set style data lines; plot 'PCDAT.~~150ps~~'; pause -1"		gnuplot -e "set xlabel 'r(Ang)'; set ylabel 'PCF'; set style data lines; plot 'PCDAT.150fs'; pause -1"
	or to a file (in the remainder we just show how to plot to a file):		or to a file (in the remainder we just show how to plot to a file):
	gnuplot -e "set terminal jpeg; set xlabel 'r(Ang)'; set ylabel 'PCF'; set style data lines; plot 'PCDAT.~~150ps~~'" > ~~PC_150ps~~.jpg		gnuplot -e "set terminal jpeg; set xlabel 'r(Ang)'; set ylabel 'PCF'; set style data lines; plot 'PCDAT.150fs'" > PC_150fs.jpg
	The obtained pair correlation function should look like in Fig. 1. Solids usually show sharp peaks in the pair correlation function since the ions only vibrate around fixed positions in the crystal lattice. In the liquid or amorphous state the distances are much more diffuse and one usually would expect no far order (but both can have near order). We see that many sharp peaks arise in the pair correlation function at higher distances, so that after 150 ps we have not molten the material.		The obtained pair correlation function should look like in Fig. 1. Solids usually show sharp peaks in the pair correlation function since the ions only vibrate around fixed positions in the crystal lattice. In the liquid or amorphous state the distances are much more diffuse and one usually would expect no far order (but both can have near order). We see that many sharp peaks arise in the pair correlation function at higher distances, so that after 150 fs we have not molten the material.


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	grep "free energy" OUTCAR\|awk ' {print $5}' > energy.dat		grep "free energy" OUTCAR\|awk ' {print $5}' > energy.dat
	We will now plot the energy using gnuplot (the user can of course use the plotting program of choice):		We will now plot the energy using gnuplot (the user can of course use the plotting program of choice):
	gnuplot -e "set terminal jpeg; set xlabel 'N_{step}'; set ylabel 'Total energy (eV/cell)';set style data lines; plot 'energy.dat'" > ~~energy_150ps~~.jpg		gnuplot -e "set terminal jpeg; set xlabel 'N_{step}'; set ylabel 'Total energy (eV/cell)';set style data lines; plot 'energy.dat'" > energy_150fs.jpg
	The progression of the total energy with respect to the length of the simulation is shown in Fig. 2. We see that the energy changes very strongly indicating very large changes in the structures. Of course this is related to the melting and it is fine.		The progression of the total energy with respect to the length of the simulation is shown in Fig. 2. We see that the energy changes very strongly indicating very large changes in the structures. Of course this is related to the melting and it is fine.

	=== 300 fs ===		=== 300 fs ===
	We repeat the calculation for another 150 ps.		We repeat the calculation for another 150 fs.
	[[File:PC ~~300ps~~.jpg\|300px\|thumb\|Fig. 3: Pair correlation functions after 300 and 150 ps.]]		[[File:PC 300fs.jpg\|300px\|thumb\|Fig. 3: Pair correlation functions after 300 and 150 fs.]]

	Before we run the calculation we need to copy the new positions and velocities in {{TAG\|CONTCAR}} to {{TAG\|POSCAR}}. Then rerun the calculation using the same {{TAG\|INCAR}} tags and command as above.		Before we run the calculation we need to copy the new positions and velocities in {{TAG\|CONTCAR}} to {{TAG\|POSCAR}}. Then rerun the calculation using the same {{TAG\|INCAR}} tags and command as above.

	*Pair correlation function:		*Pair correlation function:
	The pair correlation function after ~~300ps~~ is written to the file PCDAT.~~300ps~~ (it is evaluated only in the interval of the last 150 ps since we restarted the calculation):		The pair correlation function after 300 fs is written to the file PCDAT.300fs (it is evaluated only in the interval of the last 150 fs since we restarted the calculation):
	awk <PCDAT >PCDAT.~~300ps~~ ' NR==8 {pcskal=$1} NR==9 {pcfein=$1} NR>=13 {line=line+1; print (line-0.5)*pcfein/pcskal,$1} '		awk <PCDAT >PCDAT.300fs ' NR==8 {pcskal=$1} NR==9 {pcfein=$1} NR>=13 {line=line+1; print (line-0.5)*pcfein/pcskal,$1} '
	To compare it with the pair correlation function after 150 ps we plot them using the command:		To compare it with the pair correlation function after 150 fs we plot them using the command:
	gnuplot -e "set terminal jpeg; set xlabel 'r(Ang)'; set ylabel 'PCF'; set style data lines; plot 'PCDAT.~~150ps~~', 'PCDAT.~~300ps~~' " > ~~PC_300ps~~.jpg		gnuplot -e "set terminal jpeg; set xlabel 'r(Ang)'; set ylabel 'PCF'; set style data lines; plot 'PCDAT.150fs', 'PCDAT.300fs' " > PC_300fs.jpg
	The pair correlation functions should look like Fig. 3. We see that after 300 ps much less structure is visible at larger distances. This indicates that the melting is progressing further, but we need to continue with the monitoring of the pair correlation function until it is sufficiently converged.		The pair correlation functions should look like Fig. 3. We see that after 300 fs much less structure is visible at larger distances. This indicates that the melting is progressing further, but we need to continue with the monitoring of the pair correlation function until it is sufficiently converged.

	*Total energy:		*Total energy:
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	=== Further continuing ===		=== Further continuing ===
	We continue the calculation for 450 ps.		We continue the calculation for 450 fs.
	[[File:PC ~~750ps~~.jpg\|300px\|thumb\|Fig. 4: Pair correlation functions after 750, 300 and 150 ps.]]		[[File:PC 750fs.jpg\|300px\|thumb\|Fig. 4: Pair correlation functions after 750, 300 and 150 fs.]]
	[[File:Energy ~~750ps~~.jpg\|300px\|thumb\|Fig. 5: Energy vs number of steps in 750 ps.]]		[[File:Energy 750fs.jpg\|300px\|thumb\|Fig. 5: Energy vs number of steps in 750 fs.]]


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	*Pair correlation function:		*Pair correlation function:
	We obtain the pair correlation function using the command:		We obtain the pair correlation function using the command:
	awk <PCDAT >PCDAT.~~750ps~~ ' NR==8 {pcskal=$1} NR==9 {pcfein=$1} NR>=13 {line=line+1; print (line-0.5)*pcfein/pcskal,$1} '		awk <PCDAT >PCDAT.750fs ' NR==8 {pcskal=$1} NR==9 {pcfein=$1} NR>=13 {line=line+1; print (line-0.5)*pcfein/pcskal,$1} '

	We compare the pair correlation functions using the command:		We compare the pair correlation functions using the command:
	gnuplot -e "set terminal jpeg; set xlabel 'r(Ang)'; set ylabel 'PCF'; set style data lines; plot 'PCDAT.~~150ps~~', 'PCDAT.~~300ps~~', 'PCDAT.~~750ps~~' " > ~~PC_750ps~~.jpg		gnuplot -e "set terminal jpeg; set xlabel 'r(Ang)'; set ylabel 'PCF'; set style data lines; plot 'PCDAT.150fs', 'PCDAT.300fs', 'PCDAT.750fs' " > PC_750fs.jpg

	The pair correlation functions should look like Fig. 4. We see that for 750 ps the peak at 4 <math>\AA</math> got smoothened out compared to 300 ps but the rest of the pair correlation function didn't change much anymore. This is an indication that the calculation is converging. In principle we want to have a well equilibrated structure for a given temperature.		The pair correlation functions should look like Fig. 4. We see that for 750 fs the peak at 4 <math>\AA</math> got smoothened out compared to 300 fs but the rest of the pair correlation function didn't change much anymore. This is an indication that the calculation is converging. In principle we want to have a well equilibrated structure for a given temperature.

	*Total energy:		*Total energy:
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	grep "free energy" OUTCAR\|awk ' {print $5}' >> energy.dat		grep "free energy" OUTCAR\|awk ' {print $5}' >> energy.dat
	After that we plot the ''energy.dat'' file:		After that we plot the ''energy.dat'' file:
	gnuplot -e "set terminal jpeg; set xlabel 'N_{step}'; set ylabel 'Total energy (eV/cell)';set style data lines; plot 'energy.dat'" > ~~energy_750ps~~.jpg		gnuplot -e "set terminal jpeg; set xlabel 'N_{step}'; set ylabel 'Total energy (eV/cell)';set style data lines; plot 'energy.dat'" > energy_750fs.jpg
	The energy vs number of iteration should look like Fig. 5. We see that after a few 100 ps the energy is conserved, but of course with some fluctuations present. This should also indicate that the structure is not changing drastically anymore and that the melting is achieved. We should note that the energy conservation can be monitored because we use the deterministic {{TAG\|Nose-Hoover thermostat}} which has a kinetic and potential energy term of the heat bath which provides energy conservation. If we would use e.g. the {{TAG\|Langevin thermostat}} which is a stochastic thermostat we would obtain large fluctuations in the total energy.		The energy vs number of iteration should look like Fig. 5. We see that after a few 100 fs the energy is conserved, but of course with some fluctuations present. This should also indicate that the structure is not changing drastically anymore and that the melting is achieved. We should note that the energy conservation can be monitored because we use the deterministic {{TAG\|Nose-Hoover thermostat}} which has a kinetic and potential energy term of the heat bath which provides energy conservation. If we would use e.g. the {{TAG\|Langevin thermostat}} which is a stochastic thermostat we would obtain large fluctuations in the total energy.

	== Download ==		== Download ==