Simulations - Revision history

Homa: Create: log file and screen output

2016-04-26T23:26:39Z

Create: log file and screen output

← Older revision		Revision as of 18:26, 26 April 2016
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	* When using rerun for 2D simulations, set dimension to 2 in the input file. For the rerun command, only read in two coordinates from dump file, for example "rerun dump.dat dump x y".		* When using rerun for 2D simulations, set dimension to 2 in the input file. For the rerun command, only read in two coordinates from dump file, for example "rerun dump.dat dump x y".
	</i>		</i>

			====Log file and screen output====
			By default, LAMMPS will output basic information about your simulation (such as thermo output, neighbor list statistics, system initialization details, etc.) to a logfile and to the screen. In certain circumstances (e.g., when a simulation is restarted or the run command issued multiple times) the excess information can create unnecessary bulk in log files and screen output. The following commands (used separately or together) may be supplied on the command line when starting LAMMPS to suspend all output to the log file and/or screen:

			<pre>
			-log none -screen none
			</pre>

	== Monte Carlo simulations ==		== Monte Carlo simulations ==

Wzhwei: /* Compute RDF using 'rerun' command */

2016-04-10T04:17:08Z

Compute RDF using 'rerun' command

← Older revision		Revision as of 23:17, 9 April 2016
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	* Since the [http://lammps.sandia.gov/doc/compute_rdf.html compute rdf] command will only compute the RDF up to the interaction cutoff distance, we must change this parameter in the [http://lammps.sandia.gov/doc/pair_style.html pair_style] and [http://lammps.sandia.gov/doc/pair_coeff.html pair_coeff] commands so that we can obtain the RDF over the desired domain (i.e. if we want to compute the RDF up to a cutoff of 4.0, we would set the 'cutoff' arguments in those commands to 4.0).		* Since the [http://lammps.sandia.gov/doc/compute_rdf.html compute rdf] command will only compute the RDF up to the interaction cutoff distance, we must change this parameter in the [http://lammps.sandia.gov/doc/pair_style.html pair_style] and [http://lammps.sandia.gov/doc/pair_coeff.html pair_coeff] commands so that we can obtain the RDF over the desired domain (i.e. if we want to compute the RDF up to a cutoff of 4.0, we would set the 'cutoff' arguments in those commands to 4.0).
	* While the rerun command creates a set of atoms at every snapshot of the dumpfile that it reads, the compute rdf command expects a set of atoms to be present at the start of the rerun simulation (remember, the compute command comes before the rerun command) and will produce an error if no atoms are present. To avoid this, one can use the [http://lammps.sandia.gov/doc/create_atoms.html create atoms] command (or read in the data file via the [http://lammps.sandia.gov/doc/read_data.html read data] command) used for creating atoms in the original simulation at the beginning of the rerun.		* While the rerun command creates a set of atoms at every snapshot of the dumpfile that it reads, the compute rdf command expects a set of atoms to be present at the start of the rerun simulation (remember, the compute command comes before the rerun command) and will produce an error if no atoms are present. To avoid this, one can use the [http://lammps.sandia.gov/doc/create_atoms.html create atoms] command (or read in the data file via the [http://lammps.sandia.gov/doc/read_data.html read data] command) used for creating atoms in the original simulation at the beginning of the rerun.
			* When using rerun for 2D simulations, set dimension to 2 in the input file. For the rerun command, only read in two coordinates from dump file, for example "rerun dump.dat dump x y".
	</i>		</i>

Administrator: /* Temperature Normalization */

2015-05-15T06:26:00Z

Temperature Normalization

← Older revision		Revision as of 01:26, 15 May 2015
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	====Temperature Normalization====		====Temperature Normalization====

			By default LAMMPS normalizes the temperature by an amount ''n''<sub>dof</sub> - ''d'', where ''n''<sub>dof</sub>
	~~By default LAMMPS normalizes the temperature by an amount <math>n_\text{dof} - d</math>, where <math>n_\text{dof}</math>~~ is the system's total number of degrees of freedom and ~~<math>~~d~~</math>~~ ~~is the system's~~ dimensionality. Subtracting ~~<math>~~d~~</math>~~ accounts for the center-of-mass motion of the system. This leads to an incorrect reported value if the system has a proper frame of reference, e.g., when using a [http://lammps.sandia.gov/doc/fix_langevin.html Langevin thermostat] in which all particles interact with a stationary background solvent. In this case it is necessary to ensure <~~math~~>~~n_\text{~~dof}</~~math~~> is used instead of <~~math~~>~~n_\text{~~dof} - d~~</math>~~. To do this, use [http://lammps.sandia.gov/doc/compute_modify.html compute_modify] as follows		is the system's total number of degrees of freedom and ''d'' its dimensionality. Subtracting ''d'' accounts for the center-of-mass motion of the system. This leads to an incorrect reported value if the system has a proper frame of reference, e.g., when using a [http://lammps.sandia.gov/doc/fix_langevin.html Langevin thermostat] in which all particles interact with a stationary background solvent. In this case it is necessary to ensure ''n''<sub>dof</sub> is used instead of ''n''<sub>dof</sub> - ''d''. To do this, use [http://lammps.sandia.gov/doc/compute_modify.html compute_modify] as follows

	<pre>		<pre>

Administrator: /* Molecular dynamics simulations */

2014-12-13T05:28:50Z

Molecular dynamics simulations

← Older revision		Revision as of 00:28, 13 December 2014
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	For educational purposes, Moldy is strongly recommended, not in the least because it offers an excellent [http://ariadne.ms.northwestern.edu/Moldy/moldy-manual.pdf manual]. For class purposes, we maintain a separate list of [http://ariadne.ms.northwestern.edu/Moldy/moldy_homework.html executables] for various operating systems.		For educational purposes, Moldy is strongly recommended, not in the least because it offers an excellent [http://ariadne.ms.northwestern.edu/Moldy/moldy-manual.pdf manual]. For class purposes, we maintain a separate list of [http://ariadne.ms.northwestern.edu/Moldy/moldy_homework.html executables] for various operating systems.

	Many questions regarding ~~Lammps~~ can be resolved by consulting the [http://lammps.sandia.gov/doc/Manual.html manual], but we address some common problems below.		Many questions regarding LAMMPS can be resolved by consulting the [http://lammps.sandia.gov/doc/Manual.html manual], but we address some common problems below.

	===LAMMPS Special Usage Notes===		===LAMMPS Special Usage Notes===

Administrator at 05:26, 13 December 2014

2014-12-13T05:26:41Z

← Older revision		Revision as of 00:26, 13 December 2014
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	== Molecular dynamics simulations ==		== Molecular dynamics simulations ==

	By ~~and~~ ~~large~~ the CSML uses [http://lammps.sandia.gov/ LAMMPS] for MD, ~~though~~ depending on the application [http://www.ks.uiuc.edu/Research/namd/ NAMD], [http://www.gromacs.org/ GROMACS]~~, or any of [http://en~~.~~wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling~~ ~~a host of other packages] may be useful. Most issues can be resolved by consulting the [http://lammps.sandia.gov/doc/Manual.html LAMMPS manual], though some common problems are addressed below.~~		For many projects, the CSML uses [http://lammps.sandia.gov/ LAMMPS] for molecular dynamics, although (depending on the application) we also employ [http://www.ks.uiuc.edu/Research/namd/ NAMD] and [http://www.gromacs.org/ GROMACS].

			For educational purposes, Moldy is strongly recommended, not in the least because it offers an excellent [http://ariadne.ms.northwestern.edu/Moldy/moldy-manual.pdf manual]. For class purposes, we maintain a separate list of [http://ariadne.ms.northwestern.edu/Moldy/moldy_homework.html executables] for various operating systems.

			Many questions regarding Lammps can be resolved by consulting the [http://lammps.sandia.gov/doc/Manual.html manual], but we address some common problems below.

	===LAMMPS Special Usage Notes===		===LAMMPS Special Usage Notes===

Homa: /* Compute RDF using 'rerun' command */

2014-09-26T16:32:52Z

Compute RDF using 'rerun' command

← Older revision		Revision as of 11:32, 26 September 2014
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	</pre>		</pre>
	<i>		<i>
			Notes:
	* Since the [http://lammps.sandia.gov/doc/compute_rdf.html compute rdf] command will only compute the RDF up to the interaction cutoff distance, we must change this parameter in the [http://lammps.sandia.gov/doc/pair_style.html pair_style] and [http://lammps.sandia.gov/doc/pair_coeff.html pair_coeff] commands so that we can obtain the RDF over the desired domain (i.e. if we want to compute the RDF up to a cutoff of 4.0, we would set the 'cutoff' arguments in those commands to 4.0).		* Since the [http://lammps.sandia.gov/doc/compute_rdf.html compute rdf] command will only compute the RDF up to the interaction cutoff distance, we must change this parameter in the [http://lammps.sandia.gov/doc/pair_style.html pair_style] and [http://lammps.sandia.gov/doc/pair_coeff.html pair_coeff] commands so that we can obtain the RDF over the desired domain (i.e. if we want to compute the RDF up to a cutoff of 4.0, we would set the 'cutoff' arguments in those commands to 4.0).
	* While the rerun command creates a set of atoms at every snapshot of the dumpfile that it reads, the compute rdf command expects a set of atoms to be present at the start of the rerun simulation (remember, the compute command comes before the rerun command) and will produce an error if no atoms are present. To avoid this, one can use the [http://lammps.sandia.gov/doc/create_atoms.html create atoms] command (or read in the data file via the [http://lammps.sandia.gov/doc/read_data.html read data] command) used for creating atoms in the original simulation at the beginning of the rerun.		* While the rerun command creates a set of atoms at every snapshot of the dumpfile that it reads, the compute rdf command expects a set of atoms to be present at the start of the rerun simulation (remember, the compute command comes before the rerun command) and will produce an error if no atoms are present. To avoid this, one can use the [http://lammps.sandia.gov/doc/create_atoms.html create atoms] command (or read in the data file via the [http://lammps.sandia.gov/doc/read_data.html read data] command) used for creating atoms in the original simulation at the beginning of the rerun.

Homa: /* Compute RDF using 'rerun' command */ added note on creating atoms at the beginning of reruns

2014-09-26T16:32:22Z

Compute RDF using 'rerun' command: added note on creating atoms at the beginning of reruns

← Older revision		Revision as of 11:32, 26 September 2014
Line 38:		Line 38:
	</pre>		</pre>
	<i>		<i>
	~~Note:~~ Since the [http://lammps.sandia.gov/doc/compute_rdf.html compute rdf] command will only compute the RDF up to the interaction cutoff distance, we must change this parameter in the [http://lammps.sandia.gov/doc/pair_style.html pair_style] and [http://lammps.sandia.gov/doc/pair_coeff.html pair_coeff] commands so that we can obtain the RDF over the desired domain (i.e. if we want to compute the RDF up to a cutoff of 4.0, we would set the 'cutoff' arguments in those commands to 4.0).		* Since the [http://lammps.sandia.gov/doc/compute_rdf.html compute rdf] command will only compute the RDF up to the interaction cutoff distance, we must change this parameter in the [http://lammps.sandia.gov/doc/pair_style.html pair_style] and [http://lammps.sandia.gov/doc/pair_coeff.html pair_coeff] commands so that we can obtain the RDF over the desired domain (i.e. if we want to compute the RDF up to a cutoff of 4.0, we would set the 'cutoff' arguments in those commands to 4.0).
			* While the rerun command creates a set of atoms at every snapshot of the dumpfile that it reads, the compute rdf command expects a set of atoms to be present at the start of the rerun simulation (remember, the compute command comes before the rerun command) and will produce an error if no atoms are present. To avoid this, one can use the [http://lammps.sandia.gov/doc/create_atoms.html create atoms] command (or read in the data file via the [http://lammps.sandia.gov/doc/read_data.html read data] command) used for creating atoms in the original simulation at the beginning of the rerun.
	</i>		</i>

Homa: /* Compute RDF using 'rerun' command */

2014-09-26T16:14:33Z

Compute RDF using 'rerun' command

← Older revision		Revision as of 11:14, 26 September 2014
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	Commands from the original simulation that will not be included are ones such as dump commands and time integration fixes (e.g. fix nve; rerun only looks at single moments in time and cannot perform time integration). Fixes that constrain forces on atoms (such as fix langevin) can be invoked in general, but it does not make sense to do this for computing the RDF (even though the langevin thermostat may be employed in the original simulation).		Commands from the original simulation that will not be included are ones such as dump commands and time integration fixes (e.g. fix nve; rerun only looks at single moments in time and cannot perform time integration). Fixes that constrain forces on atoms (such as fix langevin) can be invoked in general, but it does not make sense to do this for computing the RDF (even though the langevin thermostat may be employed in the original simulation).

	As an example, let us consider computing the RDF for a typical ~~one-component shifted truncated~~ Lennard-Jones fluid past the interaction cutoff, and let us assume that we have already generated a dumpfile containing information on the atom positions over some set of timesteps. Then we will run a second simulation that reads in the particle positions from the dumpfile(s) over some subset of the original recorded timesteps ([http://lammps.sandia.gov/doc/rerun.html see arguments for the rerun command]), and will compute and output the RDF with the following commands:		As an example, let us consider computing the RDF for a typical Lennard-Jones fluid past the interaction cutoff, and let us assume that we have already generated a dumpfile containing information on the atom positions over some set of timesteps. Then we will run a second simulation that reads in the particle positions from the dumpfile(s) over some subset of the original recorded timesteps ([http://lammps.sandia.gov/doc/rerun.html see arguments for the rerun command]), and will compute and output the RDF with the following commands:
	<pre>		<pre>
	compute rdfID groupID rdf N #computes rdf with N bins		compute rdfID groupID rdf N #computes rdf with N bins

Homa: /* Compute RDF using 'rerun' command */

2014-09-26T16:14:00Z

Compute RDF using 'rerun' command

← Older revision		Revision as of 11:14, 26 September 2014
Line 31:		Line 31:
	Commands from the original simulation that will not be included are ones such as dump commands and time integration fixes (e.g. fix nve; rerun only looks at single moments in time and cannot perform time integration). Fixes that constrain forces on atoms (such as fix langevin) can be invoked in general, but it does not make sense to do this for computing the RDF (even though the langevin thermostat may be employed in the original simulation).		Commands from the original simulation that will not be included are ones such as dump commands and time integration fixes (e.g. fix nve; rerun only looks at single moments in time and cannot perform time integration). Fixes that constrain forces on atoms (such as fix langevin) can be invoked in general, but it does not make sense to do this for computing the RDF (even though the langevin thermostat may be employed in the original simulation).

	~~For~~ a typical one-component shifted truncated Lennard-Jones fluid, we will ~~read~~ in the positions of ~~particles~~ at ~~any~~ ~~number~~ of timesteps ([http://lammps.sandia.gov/doc/rerun.html see arguments for the rerun command]) ~~from~~ ~~dumpfile(s)~~ of a ~~previous~~ ~~simulation. The~~ RDF ~~is computed and output~~ with the following commands:		As an example, let us consider computing the RDF for a typical one-component shifted truncated Lennard-Jones fluid past the interaction cutoff, and let us assume that we have already generated a dumpfile containing information on the atom positions over some set of timesteps. Then we will run a second simulation that reads in the particle positions from the dumpfile(s) over some subset of the original recorded timesteps ([http://lammps.sandia.gov/doc/rerun.html see arguments for the rerun command]), and will compute and output the RDF with the following commands:
	<pre>		<pre>
	compute rdfID groupID rdf N #computes rdf with N bins		compute rdfID groupID rdf N #computes rdf with N bins

Homa: /* Compute RDF using 'rerun' command */

2014-09-26T16:06:49Z

Compute RDF using 'rerun' command

← Older revision		Revision as of 11:06, 26 September 2014
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	The 'rerun' command in LAMMPS performs a post-processing simulation by reading the atom information line-by-line from the dump file(s) created from a previous simulation. The command syntax is as follows:		The 'rerun' command in LAMMPS performs a post-processing simulation by reading the atom information line-by-line from the dump file(s) created from a previous simulation. The command syntax is as follows:
	<pre> rerun file1 file2 ... keyword args ... </pre>		<pre> rerun file1 file2 ... keyword args ... </pre>
	~~More~~ ~~information~~ can be found on the [http://lammps.sandia.gov/doc/rerun.html LAMMPS website].		A detailed description of the syntax can be found on the [http://lammps.sandia.gov/doc/rerun.html LAMMPS website].

	Besides the fact that the atoms' positions (and possibly velocities, etc.) are pre-determined from the dump file(s), we use the rerun command as if we are running a normal simulation (with some differences and limitations, explained below). When the rerun command is called, it invokes the [http://lammps.sandia.gov/doc/read_dump.html read_dump] command to read in lines from the dumpfile(s) line-by-line, each time invoking the [http://lammps.sandia.gov/doc/run.html run] command to output computed energy, forces, and any thermo output or diagnostic info the user has defined. Thus, in the input file for this pseudo simulation, we must define a system, units, dimensions, box, etc, and these will typically be identical to the original simulation.		Besides the fact that the atoms' positions (and possibly velocities, etc.) are pre-determined from the dump file(s), we use the rerun command as if we are running a normal simulation (with some differences and limitations, explained below). When the rerun command is called, it invokes the [http://lammps.sandia.gov/doc/read_dump.html read_dump] command to read in lines from the dumpfile(s) line-by-line, each time invoking the [http://lammps.sandia.gov/doc/run.html run] command to output computed energy, forces, and any thermo output or diagnostic info the user has defined. Thus, in the input file for this pseudo simulation, we must define a system, units, dimensions, box, etc, and these will typically be identical to the original simulation.