MD Files
Understanding the Output
In this chapter we shall briefly describe the output produced during a CASTEP calculation. Only the level of detail printed at iprint = 1 will be discussed.
The .castep file
Header
As well as the usual information printed at the top of the output file, the molecular dynamics data specified in the parameters file is presented.
************************ Molecular Dynamics Parameters ************************
ensemble : NPT
variable cell method : fixed basis quality
pressure : see below
temperature : 293.0 K
using : Parrinello-Rahman barostat
with characteristic cell time : 26.00 ps
using : Langevin thermostat
with characteristic ionic time : 16.95 ps
time step : 0.2000E-02 ps
number of MD steps : 500000
using best-fit first order extrapolation for wavefunctions
backup results every : 5 steps
MD SCF energy / atom convergence tol. : 0.1000E-04 eV
MD SCF convergence tolerance window : 3 cycles
*******************************************************************************
This amount of information presented in this section will obviously vary depending on the type of calculation being performed, but should be self-explanatory.
Initial cell
The information specified in the .cell file is then output. This will include the ionic positions, any user specified velocities if present, the usual pseudo-potential, k-point information, and details of any constraints. The total energy of the initial cell is then minimised, performing a finite basis set correction along the way if appropriate.
The message
is then printed, and the MD calculation proper commences. As the first time-step will require data on forces, stress (for variable cell calculations) and energies, these are evaluated and printed at this point.
Forces are output in the following format, using the force unit specified by the user, or the default of eV / Ang.
******************************** Forces *********************************
* *
* Cartesian components (eV/A) *
* --------------------------------------------------------------------- *
* x y z *
* *
* Si 1 -0.02632 -0.02632 -0.02632 *
* Si 2 -0.02653 -0.02617 -0.02617 *
* Si 3 -0.02617 -0.02617 -0.02653 *
* Si 4 -0.02617 -0.02653 -0.02617 *
* Si 5 0.00075 0.05164 0.00075 *
* Si 6 0.05204 0.05204 0.05204 *
* Si 7 0.05164 0.00075 0.00075 *
* Si 8 0.00075 0.00075 0.05164 *
* *
*************************************************************************
The stress tensor (if calculated) is output in the specified units of pressure, along with the corresponding scalar T=0 pressure, i.e. one third of the trace of the stress tensor.
***************** Stress Tensor *****************
* *
* Cartesian components (GPa) *
* --------------------------------------------- *
* x y z *
* *
* x 0.009981 1.140649 1.140649 *
* y 1.140649 0.009981 1.140649 *
* z 1.140649 1.140649 0.009981 *
* *
* Pressure: -0.0100 *
* *
*************************************************
The current time and MD energies are then printed in the user specified energy units. Here potential energy refers to the total configurational energy of electrons plus ions obtained from the DFT calculation. Kinetic energy is the classical kinetic energy of the ions. Total energy refers to the sum of these two energies.
The enthalpy and the relevant Hamiltonian energy for the ensemble as quoted in section ensembles is then printed.
The temperature is also output at this point. Note that this is the ionic temperature only. If performing a calculation with finite temperature electrons (i.e. EDFT) the electron temperature may not be the same. Finally total pressure, i.e. the trace of the stress tensor plus the kinetic (ideal gas) pressure is printed in the user specified pressure units.
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
x MD Data: x
x x
x time : 0.000000 ps x
x x
x Potential Energy: -865.882944 eV x
x Kinetic Energy: 0.265113 eV x
x Total Energy: -865.617832 eV x
x Enthalpy: -865.617735 eV x
x Hamilt Energy: -865.617735 eV x
x x
x Temperature: 293.000000 K x
x T/=0 Pressure: 0.172231 GPa x
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Iteration
The MD simulation proper now begins.
=================================================================
Starting MD iteration 1 ...
=================================================================
Following this message the current cell information on the new configuration is printed and the energy is re-minimised to determine the new forces. The MD step is then performed and the updated forces, stress and energy information is printed in the same manner as above.
-----------------------------------------------------------------
... finished MD iteration 1
-----------------------------------------------------------------
The process repeats until the calculation is killed, or the specified number of MD iterations is completed.
The .md file
The .md file is provided as a single source for all the dynamical data produced by a CASTEP calculation. In all cases, data is printed in Hartree atomic units. Fortran formating data will be given here for all entries in this file for those who wish to import it into their own analysis codes.
The CASTEP default behaviour is to record every single configuration in the .md file. This can therefore grow to quite a
large size if doing a long MD run! The only exception to this, is if doing a non-DFT calculation, whereupon a sample of the
configurations are written if md_sample_iter>0, otherwise no configurations are written.
Note that unlike the .castep file, the .md file from a previous calculation with the same seedname will be overwritten, unless the new calculation is a continuation of the original.
Header
At the top of every .md file a header is written as below. The total length is four lines including blanks. The comments written are taken from the cell/parameter files.
This is followed by a blank line. There is a single space at the start of each non-blank line. This header is written once only.
Time and Energy Data
The next entry will be the data for the first MD step. This begins with
the current time on the first line, followed by the Total, Hamiltonian, and
Kinetic energy on the second line with the label <-- E.
Formatting:
Thermodynamic Data
The current temperature is then printed with the label <-- T. If the output is from a variable cell
calculation, or calculate_stress has been explicitly set to true, the pressure
is also printed with the label <-- P.
Formatting:
Cell Data
For all calculations, the current matrix of cell vectors is printed with
the label <-- h Each row
gives the three Cartesian components of one of the cell vectors.
1.01599045E+001 0.00000000E+000 0.00000000E+000 <-- h
1.29430839E-017 1.01599045E+001 0.00000000E+000 <-- h
1.29430839E-017 1.29430839E-017 1.01599045E+001 <-- h
Formatting:
format(9x,3(3x,es18.8e3),' <-- h')
format(9x,3(3x,es18.8e3),' <-- h')
format(9x,3(3x,es18.8e3),' <-- h')
The remaining cell data is only printed for variable cell calculations, regardless
of the value of calculate_stress. First the velocity of each cell vector
is printed with the label <-- hv.
2.80052926E-008 -1.42751448E-007 -1.35787248E-007 <-- hv
-1.42751448E-007 2.76907508E-008 -1.44694219E-007 <-- hv
-1.35787248E-007 -1.44694219E-007 2.71532850E-008 <-- hv
Formatting:
format(9x,3(3x,es18.8e3),' <-- hv')
format(9x,3(3x,es18.8e3),' <-- hv')
format(9x,3(3x,es18.8e3),' <-- hv')
The full pressure tensor (including kinetic contributions) is then printed
with the label <-- S in a similar fashion.
-6.21684372E-006 3.03062374E-005 3.23291890E-005 <-- S
3.03062374E-005 -6.06171719E-006 3.31426773E-005 <-- S
3.23291890E-005 3.31426773E-005 -5.79666096E-006 <-- S
Formatting:
format(9x,3(3x,es18.8e3),' <-- S')
format(9x,3(3x,es18.8e3),' <-- S')
format(9x,3(3x,es18.8e3),' <-- S')
Ionic Data
Data on the current ionic configuration is then printed. Atoms are identified by their chemical symbol in the first column, and number of the atom within the species in the second.
First the position vectors of all ions are printed with the
label <-- R.
Si 1 1.04834750E-002 1.15560090E-002 7.82230990E-003 <-- R
Si 2 -3.20400394E-003 5.07172565E+000 5.10986361E+000 <-- R
Si 3 5.07271954E+000 5.11656710E+000 -2.45225140E-003 <-- R
Si 4 5.10789066E+000 -2.63240242E-002 5.09753015E+000 <-- R
Si 5 7.57309188E+000 2.52845762E+000 7.57612741E+000 <-- R
Si 6 2.55271297E+000 2.54057876E+000 2.53924276E+000 <-- R
Si 7 2.53422324E+000 7.64091983E+000 7.62428191E+000 <-- R
Si 8 7.63167143E+000 7.59610368E+000 2.52717191E+000 <-- R
Formatting (for each atom):
Velocities are then printed in a similar fashion.
Si 1 5.77278549E-005 7.23673746E-005 4.30349159E-005 <-- V
Si 2 -1.72415752E-005 -5.23270551E-005 1.75385181E-004 <-- V
Si 3 -4.17085102E-005 2.14539848E-004 -1.78769096E-005 <-- V
Si 4 1.58756714E-004 -1.60916056E-004 9.49147966E-005 <-- V
Si 5 -2.70431102E-004 -7.18757382E-005 -2.43440176E-004 <-- V
Si 6 7.51663795E-005 8.70332331E-008 -8.82271461E-006 <-- V
Si 7 -4.19898677E-005 1.31687892E-004 3.60873179E-005 <-- V
Si 8 7.97201068E-005 -1.33563298E-004 -7.92824105E-005 <-- V
Formatting (for each atom):
Finally forces are printed.
Si 1 -4.23569381E-003 2.52214252E-003 -2.46018145E-003 <-- F
Si 2 3.06338418E-003 -2.16206923E-003 -5.29928454E-003 <-- F
Si 3 7.37259995E-004 -4.73479365E-003 -2.20030945E-003 <-- F
Si 4 -6.89050954E-003 -2.25153379E-003 -8.37626756E-003 <-- F
Si 5 4.53551291E-003 3.34757083E-003 1.02791157E-002 <-- F
Si 6 2.06737343E-003 2.05175887E-003 2.70990363E-003 <-- F
Si 7 -1.41457164E-003 -9.15433604E-004 1.54850432E-003 <-- F
Si 8 2.13724448E-003 2.14235805E-003 3.79851935E-003 <-- F
Formatting (for each atom):
A blank line is then printed, and the process repeats with the data from the next time-step.
The .hug file
If you are using the Hugoniostat predictor-corrector method to generate a Hugoniot curve, each different state point
generated has a different compression etc. This is summarized in the .hug file as follows:
0.990000000000 36.31531287 0.41888602 0.15771481 <-- cTPE
0.943272613764 40.07750465 0.63662992 1.62298398 <-- cTPE
0.865294155381 58.07130958 1.30346964 6.92736406 <-- cTPE
The 4 data fields are:
c - the ratio of the compressed to original cell vectors
T - the temperature (in user units) - calculated as a time average of the instantaneous temperature of the configurations at this compression
P - the pressure (in user units) - calculated as a time average
E - the energy (in user units) - calculated as a time average