The OUTPUT Files¶

DL_POLY_5 may produce many output files. However only OUTPUT (an incremental summary file of the simulation), STATIS (a statistical history file), REVCON (a restart configuration file - final) and REVIVE (a restart statistics accumulators file - final) are mandatory. DUMP_E (a restart electronic temperature grid file - final) is also produced if the two-temperature model (TTM) is in use. The existence of the remaining files is optional upon user specifications in CONTROL. Some of these optional files are HISTORY, DEFECTS, MSDTMP, CFGMIN, RDFDAT, USRDAT, ZDNDAT, VDFDAT, LATS_E, LATS_I, PEAK_E, PEAK_I. These respectively contain: an incremental dump file of all atomic coordinates, velocities and forces; an incremental dump file of atomic coordinates of defected particles (interstitials) and sites (vacancies); an incremental dump file of of individual atomic mean square displacement and temperature; a dump file of all atomic coordinates of a minimised structure; a radial distribution function (RDF) data file; the RDF data file for the umbrella sampling (harmonic restraint); Z-density distribution data file; velocity autocorrelation function (VAF) data files (one file for each species); electronic temperature profile data file; ionic temperature profile data file; electronic temperature statistical data file; ionic temperature statistical data file.

The HISTORY File¶

The HISTORY file is the dump file of atomic coordinates, velocities and forces. Its principal use is for off-line analysis. The file is written by the subroutine trajectory_write. The control variables for this file are ltraj, nstraj, istraj and keytrj which are created internally, based on information read from the traj directive in the CONTROL file (see Section The CONTROL File). The HISTORY file will be created only if the directive traj appears in the CONTROL file.

The HISTORY file can become very large, especially if it is formatted. For serious simulation work it is recommended that the file be written to a scratch disk capable of accommodating a large data file. Alternatively, the file may be written in netCDF format instead of in ASCII (users must change ensure this functionality is available), which has the additional advantage of speed.

The HISTORY has the following structure:

record 1
header    a72       file header
record 2
keytrj    integer   trajectory key (see Table [keytrj]) in last frame
imcon     integer   periodic boundary key (see Table (7)) in last frame
megatm    integer   number of atoms in simulation cell in last frame
frame     integer   number of configuration frames in file
records   integer   number of records in file

For timesteps greater than nstraj the HISTORY file is appended at intervals specified by the traj directive in the CONTROL file, with the following information for each configuration:

record i
timestep    a8        the character string “timestep”
nstep       integer   the current time-step
megatm      integer   number of atoms in simulation cell (again)
keytrj      integer   trajectory key (again)
imcon       integer   periodic boundary key (again)
tstep       real      integration timestep (ps)
time        real      elapsed simulation time (ps)
record ii
cell(1)     real      x component of a cell vector in Å (or DPD length units)
cell(2)     real      y component of a cell vector in Å (or DPD length units)
cell(3)     real      z component of a cell vector in Å (or DPD length units)
record iii
cell(4)     real      x component of b cell vector in Å (or DPD length units)
cell(5)     real      y component of b cell vector in Å (or DPD length units)
cell(6)     real      z component of b cell vector in Å (or DPD length units)
record iv
cell(7)     real      x component of c cell vector in Å (or DPD length units)
cell(8)     real      y component of c cell vector in Å (or DPD length units)
cell(9)     real      z component of c cell vector in Å (or DPD length units)

This is followed by the configuration for the current timestep. i.e. for each atom in the system the following data are included:

record a
atmnam    a8        atomic label
iatm      integer   atom index
weight    real      atomic mass (a.m.u.)
charge    real      atomic charge (e)
rsd       real      displacement from position at t = 0 in Å (or DPD length units)
record b
xxx       real      x coordinate
yyy       real      y coordinate
zzz       real      z coordinate
record c only for keytrj > 0
vxx       real      x component of velocity in Å/picosecond (or DPD velocity units)
vyy       real      y component of velocity in Å/picosecond (or DPD velocity units)
vzz       real      z component of velocity in Å/picosecond (or DPD velocity units)
record d only for keytrj > 1
fxx       real      x component of force in Å\(\cdot\)Dalton/picosecond\(^{2}\) (or DPD force units)
fyy       real      y component of force in Å\(\cdot\)Dalton/picosecond\(^{2}\) (or DPD force units)
fzz       real      z component of force in Å\(\cdot\)Dalton/picosecond\(^{2}\) (or DPD force units)

Thus the data for each atom is a minimum of two records and a maximum of 4.

The MSDTMP File¶

The MSDTMP file is the dump file of individual atomic mean square displacements (square roots in Å) and mean square temperature (square roots in Kelvin). Its principal use is for off-line analysis. The file is written by the subroutine msd_write. The control variables for this file are l_msd, nstmsd, istmsd which are created internally, based on information read from the msdtmp directive in the CONTROL file (see Section The CONTROL File). The MSDTMP file will be created only if the directive msdtmp appears in the CONTROL file.

The MSDTMP file can become very large, especially if it is formatted. For serious simulation work it is recommended that the file be written to a scratch disk capable of accommodating a large data file.

The MSDTMP has the following structure:

record 1
header    a52       file header
record 2
megatm    integer   number of atoms in simulation cell in last frame
frame     integer   number configuration frames in file
records   integer   number of records in file

For timesteps greater than nstmsd the MSDTMP file is appended at intervals specified by the msdtmp directive in the CONTROL file, with the following information for each configuration:

record i
timestep    a8 the      character string “timestep”
nstep       integer     the current time-step
megatm      integer     number of atoms in simulation cell (again)
tstep       real        integration timestep (ps or DPD time units)
time        real        elapsed simulation time (ps or DPD time units)

This is followed by the configuration for the current timestep. i.e. for each atom in the system the following data are included:

record a
atmnam    a8        atomic label
iatm      integer   atom index \(\sqrt{\texttt{MSD}(t)}\) real square root of the atomic mean square displacements (in Å or DPD length units)
T(mean)       real      atomic mean temperature (in Kelvin or DPD temperature units)

The DEFECTS File¶

The DEFECTS file is the dump file of atomic coordinates of defects (see Section The REFERENCE File<reference-file>). Its principal use is for off-line analysis. The file is written by the subroutine defects_write. The control variables for this file are ldef, nsdef, isdef and rdef which are created internally, based on information read from the defects directive in the CONTROL file (see Section The CONTROL File). The DEFECTS file will be created only if the directive defects appears in the CONTROL file.

The DEFECTS file may become very large, especially if it is formatted. For serious simulation work it is recommended that the file be written to a scratch disk capable of accommodating a large data file.

The DEFECTS has the following structure:

record 1
header    a72       file header
record 2
rdef      real      site-interstitial cutoff (Å or DPD length units) in last frame
frame     integer   number configuration frames in file
records   integer   number of records in file

For timesteps greater than nsdef the DEFECTS file is appended at intervals specified by the defects directive in the CONTROL file, with the following information for each configuration:

record i
timestep      a8        the character string “timestep”
nstep         integer   the current time-step
tstep         real      integration timestep (ps or DPD time units)
time          real      elapsed simulation time (ps or DPD time units)
imcon         integer   periodic boundary key (see Table (7))
rdef          real      site-interstitial cutoff (Å or DPD length units)
record ii
defects       a7        the  character string “defects”
ndefs         integer   the total number of defects
interstitials a13       the character string “interstitials”
ni            integer   the total number of interstitials
vacancies     a9        the character string “vacancies”
nv            integer   the total number of vacancies
record iii
cell(1)       real      x component of a cell vector
cell(2)       real      y component of a cell vector
cell(3)       real      z component of a cell vector
record iv
cell(4)       real      x component of b cell vector
cell(5)       real      y component of b cell vector
cell(6)       real      z component of b cell vector
record v
cell(7)       real      x component of c cell vector
cell(8)       real      y component of c cell vector
cell(9)       real      z component of c cell vector

This is followed by the ni interstitials for the current timestep, as each interstitial has the following data lines:

record a
atmnam    a10       i_atomic label from CONFIG
iatm      integer   atom index from CONFIG
record b
xxx       real      x coordinate
yyy       real      y coordinate
zzz       real      z coordinate

This is followed by the nv vacancies for the current timestep, as each vacancy has the following data lines:

record a
atmnam  a10       v_atomic label from REFERENCE
iatm    integer   atom index from REFERENCE
record b
xxx     real      x coordinate from REFERENCE
yyy     real      y coordinate from REFERENCE
zzz     real      z coordinate from REFERENCE

The RSDDAT File¶

The RSDDAT file is the dump file of atomic coordinates of atoms that are displaced from their original position at $t~=~0$ farther than a preset cutoff. Its principal use is for off-line analysis. The file is written by the subroutine rsd_write. The control variables for this file are lrsd, nsrsd, isrsd and rrsd which are created internally, based on information read from the displacements directive in the CONTROL file (see Section The CONTROL File). The RSDDAT file will be created only if the directive defects appears in the CONTROL file.

The RSDDAT file may become very large, especially if it is formatted. For serious simulation work it is recommended that the file be written to a scratch disk capable of accommodating a large data file.

The RSDDAT has the following structure:

record 1
header    a72       file header
record 2
rdef      real      displacement qualifying cutoff (Å or DPD length units) in last frame
frame     integer   number configuration frames in file
records   integer   number of records in file

For timesteps greater than nsrsd the RSDDAT file is appended at intervals specified by the displacements directive in the CONTROL file, with the following information for each configuration:

record i
timestep        a8        the character string “timestep”
nstep           integer   the current time-step
tstep           real      integration timestep (ps or DPD time units)
time            real      elapsed simulation time (ps or DPD time units)
imcon           integer   periodic boundary key (see Table (7))
rrsd            real      displacement qualifying cutoff (Å or DPD length units)
record ii
displacements   a13       the character string “displacements”
nrsd            integer   the total number of displacements
record iii
cell(1)         real      x component of a cell vector
cell(2)         real      y component of a cell vector
cell(3)         real      z component of a cell vector
record iv
cell(4)         real      x component of b cell vector
cell(5)         real      y component of b cell vector
cell(6)         real      z component of b cell vector
record v
cell(7)         real      x component of c cell vector
cell(8)         real      y component of c cell vector
cell(9)         real      z component of c cell vector

This is followed by the nrsd displacements for the current timestep, as each atom has the following data lines:

record a
atmnam    a10       atomic label from CONFIG
iatm      integer   atom index from CONFIG
ratm      real      atom displacement from its position at \(t~=~0\)
record b
xxx       real      x coordinate
yyy       real      y coordinate
zzz       real      z coordinate

The CFGMIN File¶

The CFGMIN file only appears if the user has selected the programmed minimisation option (directive minimise (or optimise) in the CONTROL file). Its contents have the same format as the CONFIG file (see Section The CONFIG File), but contains only atomic position data and will never contain either velocity or force data (i.e. parameter levcfg is always zero). In addition, three extra numbers appear on the end of the second line of the file:

an integer indicating the number of minimisation cycles required to obtain the structure,
the configuration energy of the minimised configuration expressed in DL_POLY_5 units (Section [units]), and
the configuration energy of the initial structure expressed in DL_POLY_5 units (Section [units]).

The OUTPUT File¶

The job output consists of 7 sections: Header; Simulation control specifications; Force field specification; System specification; Summary of the initial configuration; Simulation progress; Sample of the final configuration; Summary of statistical data; and Radial distribution functions and Z-density profile. These sections are written by different subroutines at various stages of a job. Creation of the OUTPUT file always results from running . It is meant to be a human readable file, destined for hardcopy output.

Simulation Control Specifications¶

Echoes the input from the CONTROL file. Some variables may be reset if illegal values were specified in the CONTROL file. This part of the file is written from the subroutine read_control.

Force Field Specification¶

Echoes the FIELD file. A warning line will be printed if the system is not electrically neutral. This warning will appear immediately before the non-bonded short-range potential specifications. This part of the file is written from the subroutine read_field.

System Specification¶

Echoes system name, periodic boundary specification, the cell vectors and volume, some initial estimates of long-ranged corrections the energy and pressure (if appropriate), some concise information on topology and degrees of freedom break-down list. This part of the file is written from the subroutines scan_config, check_config, system_init, report_topology and set_temperature.

Summary of the Initial Configuration¶

This part of the file is written from the main subroutine dl_poly_. It states the initial configuration of (a maximum of) 20 atoms in the system. The configuration information given is based on the value of levcfg in the CONFIG file. If levcfg is 0 (or 1) positions (and velocities) of the 20 atoms are listed. If levcfg is 2 forces are also written out.

Simulation Progress¶

This part of the file is written by the DL_POLY_5 root segment dl_poly. The header line is printed at the top of each page as:

--------------------------------------------------------------------------------------------------

    step   eng_tot  temp_tot   eng_cfg   eng_src   eng_cou   eng_bnd   eng_ang   eng_dih   eng_tet
time(ps)    eng_pv  temp_rot   vir_cfg   vir_src   vir_cou   vir_bnd   vir_ang   vir_con   vir_tet
cpu  (s)    volume  temp_shl   eng_shl   vir_shl     alpha      beta     gamma   vir_pmf     press

--------------------------------------------------------------------------------------------------

The labels refer to :

line 1
step         MD step number
eng_tot     total internal energy of the system
temp_tot    system temperature (in Kelvin or DPD temperature units)
eng_cfg     configurational energy of the system
eng_src     configurational energy due to short-range potential contributions
eng_cou     configurational energy due to electrostatic potential
eng_bnd     configurational energy due to chemical bond potentials
eng_ang     configurational energy due to valence angle and three-body potentials
eng_dih     configurational energy due to dihedral inversion and four-body potentials
eng_tet     configurational energy due to tethering potentials
line 2
time(ps)    elapsed simulation time (in pico-seconds or DPD time units) since the beginning of the job
eng_pv      enthalpy of system
temp_rot    rotational temperature (in Kelvin or DPD temperature units)
vir_cfg     total configurational contribution to the virial
vir_src     short range potential contribution to the virial
vir_cou     electrostatic potential contribution to the virial
vir_bnd     chemical bond contribution to the virial
vir_ang     angular and three-body potentials contribution to the virial
vir_con     constraint bond contribution to the virial
vir_tet     tethering potential contribution to the virial
line 3
cpu (s)     elapsed cpu time (in seconds) since the beginning of the job
volume      system volume (in Å\(^{3}\) or cubic DPD length units)
temp_shl    core-shell temperature (in Kelvin or DPD temperature units)
eng_shl     configurational energy due to core-shell potentials
vir_shl     core-shell potential contribution to the virial
alpha       angle between b and c cell vectors (in degrees)
beta        angle between c and a cell vectors (in degrees)
gamma       angle between a and b cell vectors (in  degrees)
vir_pmf     PMF constraint contribution to the virial
press       pressure (in kilo-atmospheres)

Note: The total internal energy of the system (variable tot_energy) includes all contributions to the energy (including system extensions due to thermostats etc.). It is nominally the conserved variable of the system, and is not to be confused with conventional system energy, which is a sum of the kinetic and configuration energies.

The interval for printing out these data is determined by the directive print in the CONTROL file. At each time-step that printout is requested the instantaneous values of the above statistical variables are given in the appropriate columns. Immediately below these three lines of output the rolling averages of the same variables are also given. The maximum number of time-steps used to calculate the rolling averages is controlled by the directive stack in file CONTROL (see above) and listed as parameter mxstak in the setup_module file (see Section File Structure). The default value is mxstak $=~100$.

Energy Units¶

The energy unit for the energy and virial data appearing in the OUTPUT is defined by the units directive appearing in the FIELD file. System energies are therefore read in units per MD cell.

Pressure Units¶

The unit of pressure is katms for all energy units apart from DPD, which uses energy per cubic DPD length unit.

Two-Temperature Model¶

If the two-temperature model is in use, information about the timestep sizes used for electronic thermal diffusivity is written immediately prior to each report of statistical variables at each molecular dynamics timestep for which printout is requested. The optimum diffusive timestep size is given in pico-seconds, along with the chosen value and the corresponding number of divisions of the MD timestep. If dynamic calculation of the average atomic density in active cells is requested, this value is included along with the number of active ionic temperature cells. Reports are also given when energy deposition starts and finishes. (Note that this functionality assumes atomistic modelling is in use, so DPD units cannot be used for two-temperature simulations.)

Sample of Final Configuration¶

The positions, velocities and forces of the 20 atoms used for the sample of the initial configuration (see above) are given. This is written by the main subroutine dl_poly.

Summary of Statistical Data¶

This portion of the OUTPUT file is written from the subroutine statistics_result. The number of time-steps used in the collection of statistics is given. Then the averages over the production portion of the run are given for the variables described in the previous section. The root mean square variation in these variables follow on the next two lines. The energy and pressure units are as for the preceding section.

The Cauchy stress or pressure tensor is then provided, giving average values and root mean squared variations for all nine components, all in units of pressure. If a DPD thermostat was in use, separated pressure tensors resulting from conservative (configurational), dissipative, random and kinetic contributions are then provided: again the mean values for each component and the root mean squared variations are displayed in pressure units.

Also provided in this section are estimates of the diffusion coefficient and the mean square displacement for the different atomic species in the simulation. These are determined from a single time origin and are therefore approximate. Accurate determinations of the diffusion coefficients can be obtained using the msd utility program, which processes the HISTORY file (see User Manual).

If an NPT (N$\sigma$T) simulation is performed the OUTPUT file also provides the mean pressure (and stress tensor in pressure units as density) and mean simulation cell vectors. In case when extended N$\underline{\underline{\mathbf{\sigma}}}$T ensembles are used then further mean $(x,y)$ plain area and mean surface tension are also displayed in the OUTPUT file.

Radial Distribution Functions¶

If both calculation and printing of radial distribution functions have been requested (by selecting directives rdf_calculate and rdf_print in the CONTROL file) radial distribution functions are printed out. This is written from the subroutine rdf_compute. First the number of time-steps used for the collection of the histograms is stated.

For each function a header line states the atom types (‘a’ and ‘b’) represented by the function. Then $r, g(r)$ and $n(r)$ are given in tabular form. $n(r)$ is the average number of atoms of type ‘b’ within a sphere of radius $r$ around an atom of type ‘a’. Note that a readable version of these data is provided by the RDFDAT file (below).

Umbrella Sampling Restraint RDF¶

If an umbrella sampling harmonic restraint is defined in the FIELD file (by selecting the ushr external field sectione) the RDF of the two restraint objects/fragments is printed out. This is written from the subroutine usr_compute in rdf_compute. Note that a readable version of these data is provided by the USRDAT file (below).

Z-density Profile¶

If both calculation and printing of Z-density profiles have been requested (by selecting directives zden_calculate and zden_print in the CONTROL file) Z-density profiles are printed out as the last part of the OUTPUT file. This is written by the subroutine z_density_compute. First the number of time-steps used for the collection of the histograms is stated. Then each function is given in turn. For each function a header line states the atom type represented by the function. Then $z,~\rho(z)$ and $n(z)$ are given in tabular form. Output is given from $Z = [-L/2,L/2]$ where L is the length of the MD cell in the Z direction and $\rho(z)$ is the mean number density. $n(z)$ is the running integral from $-L/2$ to $z$ of $({\rm xy~cell~area}) \times \rho(s)~ds$. Note that a readable version of these data is provided by the ZDNDAT file (below).

Velocity Autocorrelation Functions¶

If both calculation and printing of velocity autocorrelation functions have been requested (by selecting directives vaf_calculate and vaf_print in the CONTROL file) the velocity autocorrelation function for the system (either time-averaged or the last complete sample) is printed out as the last part of the OUTPUT file. This is written by the subroutine vaf_compute. First the details of the calculations are stated: either the number of samples used to give a time-averaged profile or the number of the last completed sample with its starting time. The absolute value of the velocity autocorrelation function for the system at $t=0$, $C(0)$, is then stated. Then $t$ and $Z(t)$ are given in tabular form. $Z(t)=C(t)/C(0)$ is the value of the velocity autocorrelation function, $C(t)=\langle \underline{v}_{i}(0) \cdot \underline{v}_{i}(t) \rangle$, scaled by $C(0) \equiv 3k_B T/m$. Note that a readable version of these data for individual species is provided by the VAFDAT files (below).

The HEATFLUX File¶

The HEATFLUX file contains data relevant to the calculation of heat-flux via a Green-Kubo mothod via an external convolution, the information is written as:

STEP  STPTMP   VOLUME   HEAT_FLUX

The PP_CONT File¶

This file contains the contributions of each particle to energies, forces and stresses in a format similar to to the CONFIG file, but with ID replaced with energy, and velocities/forces with the stress 6-vector.

TAG  ATMNAM  KIN_E  MASS ENERGY
STR_XX  STR_YX  STR_ZX
STR_XY  STR_YY  STR_ZY
STR_XZ  STR_YZ  STR_ZZ

The REVCON File¶

This file is formatted and written by the subroutine revive. REVCON is the restart configuration file. The file is written every ndump time steps in case of a system crash during execution and at the termination of the job. A successful run of DL_POLY_5 will always produce a REVCON file, but a failed job may not produce the file if an insufficient number of timesteps have elapsed. ndump is controlled by the directive data_dump_frequency in file CONTROL (see above) and listed as parameter ndump in the setup_module file (see Section File Structure). The default value is ndump $=1000$.

REVCON is identical in format to the CONFIG input file (see Section The CONFIG File) with the addition of the step number, timestep, and simulation time (steps * timestep) on the 2nd meta-data line. I.e the first two lines of a REVCON will read

record 1
header      a72       title line

record 2
levcfg      integer   CONFIG file key. See Table (6) for permitted values
imcon       integer   Periodic boundary key. See Table (7) for permitted values
megatm      integer   Total number of particles (crystalographic entities)
step        integer   Simulation step this REVCON was written.
tstep       real      Simulation time-step.
time        real      Simulation time (steps * timestep).

REVCON should be renamed CONFIG to continue a simulation from one job to the next. This is done for you by the copy macro supplied in the execute directory of .

The REVIVE File¶

This file is unformatted and written by the subroutine system_revive. It contains the accumulated statistical data. It is updated whenever the file REVCON is updated (see previous section). REVIVE should be renamed REVOLD to continue a simulation from one job to the next. This is done by the copy macro supplied in the execute directory of . In addition, to continue a simulation from a previous job the restart keyword must be included in the CONTROL file.

The format of the REVIVE file is identical to the REVOLD file described in Section The REVOLD File.

The DUMP_E File¶

This file is formatted and written by the subroutine ttm_system_revive every ndump time steps. It contains the electronic temperatures of all coarse-grained electronic temperature (CET) cells and can be used to restart a simulation using the two-temperature model without renaming the file.

The format of the DUMP_E is described in Section The DUMP_E File.

The RDFDAT File¶

This is a formatted file containing Radial Distribution Function (RDF) data. Its contents are as follows:

record 1
cfgname   a72       configuration name
record 2
ntprdf    integer   number of different RDF pairs tabulated in file
mxgrdf    integer   number of grid points for each RDF pair

There follow the data for each individual RDF, i.e. ntprdf times. The data supplied are as follows:

first record
atname 1  a8      first atom name
atname 2  a8      second atom name
following records (mxgrdf records)
radius    real    interatomic distance (Å or DPD length unit)
g(r)      real    RDF at given radius
n(r)      real    RDF at given radius

Note 1. The RDFDAT file is optional and appears when the rdf_print option is specified in the CONTROL file.

Note 2. Along with the RDFDAT file, two other files will be created whenever the analysis directives are invoked: VDWPMF & VDWTAB, both containing the data for potentials of mean force and the corresponding virials calculated based on the obtained RDF:s, i.e. PMF $\sim -\ln({\rm RDF})$ (in the energy units specified in the FIELD file). These files have a simple three column format, the same as that used for *PMF files in the case of bonded units, see Section Intramolecular Probability Distribution Function (PDF) Analysis. The purpose of these files is to provide the user with means of setting up a PMF-based force-field, for example in the case of initial coarse-graining of an atomistic system. In particular, one can convert the VDWTAB file into a correctly formatted TABVDW file (Section The TABVDW File) by using the utility called pmf2tab.f (subject to compilation; found in DL_POLY_5 directory utility) as follows,

[user@host]$ pmf2tab.exe < VDWTAB

see Section User-Defined Coarse-Grain Models with Tabulated Force-Fields for completeness.

The USRDAT File¶

record 1
# title   a100      file header title
record 2
# header  a100      file information header
record 3
# info    a30       information to follow string
record 3
bins      integer   number of bins
cutoff    real      cutoff in Å (or DPD length unit)
frames    integer   number of sampled configurations
volume    real      average cell volume Å\(^{3}\) (or cubic DPD length units)
record 4
#         a1        a hash (#) symbol
following records (mxgusr records)
radius    real      interatomic distance (Å or DPD length unit)
g(r)      real      RDF at given radius

The ZDNDAT File¶

This is a formatted file containing the Z-density data. Its contents are as follows:

record 1
cfgname   a72       configuration name
record 2
ntpatm    integer   number of unique atom types profiled in file
mxgrdf    integer   number of grid points in the Z-density function

There follow the data for each individual Z-density function, i.e. ntpatm times. The data supplied are as follows:

first record
atname    a8    unique atom name
following records (mxgrdf records)
z         real  distance in z direction (Å or DPD length units)
\(\rho(z)\) real Z-density at given height z
:math: n(z) real rolling Z-density integral at given height z

Note the ZDNDAT file is optional and appears when the zden_print option is specified in the CONTROL file.

The VAFDAT Files¶

These are formatted files containing Velocity Autocorrelation Function (VAF) data. An individual file is created for each atomic species, i.e. VAFDAT_atname. Their contents are as follows:

record
cfgname   a72   configuration name

There follow the data for the VAF, either a single time-averaged profile or successive profiles separated by two blank lines. The data supplied are as follows:

first record
atname    a8        atom name
binvaf    integer   number of data points in VAF profile, excluding \(t=0\)
vaforigin real      absolute value of VAF at \(t=0\)  (\(C(0) \equiv 3k_B T/m\))
vaftime0  real      simulation time (ps or DPD time units) at beginning of (last) VAF profile (\(t=0\))
following records (binvaf+1 records)
t         real      time (ps or DPD time units)
Z(t)      real      scaled velocity autocorrelation function (\(C(t)/C(0)\)) at given time \(t\)

Note the VAFDAT files are optional and appear when the vaf_print option is specified in the CONTROL file.

The INTDAT, INTPMF & INTTAB Files¶

These files, where INT is referring to INTra-molecular interactions and VDW(RDF derived inter-molecular), have very similar formatting rules with some examples shown in Section Intramolecular Probability Distribution Function (PDF) Analysis. Refer to Section Intramolecular Probability Distribution Function (PDF) Analysis for their meaning and usage in coarse grained model systems.

record 1
# title     a100        file header title
record 2
# header    a100        file information header
record 3
# info      a30         information to follow string
bins        integer     number of bins for all PDFs
cutoff      real        cutoff in Å (or DPD length units) for bonds and RDFs or degrees for angular intramolecular interactions
frames      integer     number of sampled configurations
types       integer     number of unique types of these interactions
record 4
#           a1          a hash (#) symbol
record 5
# info 1    a100        information to follow string
record 6
#           a1          a hash (#) symbol

The subsequent records define each PDF potential in turn, in the order indicated by the specification in the FIELD file. Each potential is defined by a header record and a set of data records with the potential-like and force-like tables.

empty record:
id record:
# info    a25     information to follow string
atom 1    a8      first atom type
atom 2    a8      second atom type
atom 3    a8      third atom type - only available in ANG* files
atom 4    a8      forth atom type - only available in DIH* & INV* files
index     integer unique index of PDF in file
instances integer instances of this unique type of PDF
interaction data records 1–bins:
abscissa  real    consecutive value over the full cutoff/range in Å for BNDTAB & VDWTAB and degrees for ANGTAB, DIHTAB & INVTAB
potential real    potential at the abscissa grid point in units as specified in FIELD
force     real    complementary force (virial for BNDTAB & VDWTAB) value

The STATIS File¶

The file is formatted, with integers as “i10” and reals as “e14.6”. It is written by the subroutine statistics_collect. It consists of two header records followed by many data records of statistical data.

record 1
cfgname   a72   configuration name
record 2
string    a8    energy units

Data records¶

Subsequent lines contain the instantaneous values of statistical variables dumped from the array stpval. A specified number of entries of stpval are written in the format “(1p,5e14.6)”. The number of array elements required (determined by the parameter mxnstk in the setup_module file) is

\[\begin{split}\begin{aligned} \texttt{mxnstk} \ge ~& 28 + 9~(\rm stress~tensor~elements) ~+ \nonumber \\ & 36~(\rm separated~stress~tensor~elements) ~+ \nonumber \\ & \texttt{ntpatm}~(\rm number~of~unique~atomic~sites) ~+ \nonumber \\ & 10~(\rm if~constant~pressure~simulation~requested) ~+ \nonumber \\ & 2~(\rm if~iso~>~0~requested) + 2~(\rm if~iso~>~1~requested) ~+ \nonumber \\ & 2*mxatdm~(\rm if~msdtmp~option~is~used) \nonumber\end{aligned}\end{split}\]

The STATIS file is appended at intervals determined by the stats directive in the CONTROL file. The energy unit is as specified in the FIELD file with the units directive, and are compatible with the data appearing in the OUTPUT file. The contents of the appended information of calculated instantaneous observables is:

record i
nstep         integer   current MD time-step
time          real      elapsed simulation time
nument        integer   number of array elements to follow
record ii stpval(1) – stpval(5)
engcns        real      total extended system energy, \(E^{x}_{tot}=(E_{kin}+E_{rot})+E_{conf}+E_{consv}\) (i.e. including the conserved quantity, \(E_{consv}\))
temp          real      system temperature, \(2\frac{E_{kin}+E_{rot}}{f k_{B}}\)
engcfg        real      configurational energy, \(E_{conf}\)
engsrc        real      short range potential energy
engcpe        real      electrostatic energy
record iii stpval(6) – stpval(10)
engbnd        real      chemical bond energy
engang        real      valence angle and 3-body potential energy
engdih        real      dihedral, inversion, and 4-body potential energy
engtet        real      tethering energy
enthal        real      enthalpy (\(E^{x}_{tot} + {\cal P} \cdot V\)) for NVE/T/E\(_{kin}\) ensembles
enthalpy (\(E^{x}_{tot} + P \cdot {\cal V}\)) for NP/\(\sigma\)T or NP\(_{n}\)A/\(\gamma\) ensembles
record iv stpval(11) – stpval(15)
tmprot        real      rotational temperature, \(E_{rot}\)
vir           real      total virial
virsrc        real      short-range virial
vircpe        real      electrostatic virial
virbnd        real      bond virial
record v stpval(16) – stpval(20)
virang        real      valence angle and 3-body virial
vircon        real      constraint bond virial
virtet        real      tethering virial
volume        real      volume, \({\cal V}\)
tmpshl        real      core-shell temperature
record vi stpval(21) – stpval(25)
engshl        real      core-shell potential energy
virshl        real      core-shell virial
alpha         real      MD cell angle \(\alpha\)
beta          real      MD cell angle \(\beta\)
gamma         real      MD cell angle \(\gamma\)
record vii stpval(26), stpval(27), stpval(0)
virpmf        real      PMF constraint virial
press         real      pressure, \({\cal P}\)
consv         real      extended DoF energy, \(E_{consv}\)
the next 9 entries for the stress tensor in pressure units
stress(1)     real      xx component of stress tensor
stress(2)     real      xy component of stress tensor
stress(3)     real      xz component of stress tensor
stress(4)     real      yx component of stress tensor
...           real      ...
stress(9)     real      zz component of stress tensor
the next 36 entries for separated contributions of the stress tensor in pressure units - if a simulation with DPD is undertaken
strcon(1)     real      xx component of conservative contribution to stress tensor
strcon(2)     real      xy component of conservative contribution to stress tensor
strcon(3)     real      xz component of conservative contribution to stress tensor
strcon(4)     real      yx component of conservative contribution to stress tensor
...           real      ...
strcon(9)     real      zz component of conservative contribution to stress tensor
strdis(1)     real      xx component of dissipative contribution to stress tensor
strdis(2)     real      xy component of dissipative contribution to stress tensor
...           real      ...
strdis(9)     real      zz component of dissipative contribution to stress tensor
strran(1)     real      xx component of random contribution to stress tensor
strran(2)     real      xy component of random contribution to stress tensor
...           real      ...
strran(9)     real      zz component of random contribution to stress tensor
strkin(1)     real      xx component of kinetic contribution to stress tensor
strkin(2)     real      xy component of kinetic contribution to stress tensor
...           real      ...
strkin(9)     real      zz component of kinetic contribution to stress tensor
the next ``ntpatm`` entries
amsd(1)       real      mean squared displacement of first atom types
amsd(2)       real      mean squared displacement of second atom types
... ... ...
amsd(ntpatm)  real      mean squared displacement of last atom types
the next 10 entries - if a NPT or N:math:`mat{sigma}`T simulation is undertaken
cell(1)       real      x component of a cell vector
cell(2)       real      y component of a cell vector
cell(3)       real      z component of a cell vector
cell(4)       real      x component of b cell vector
...           real      ...
cell(9)       real      z component of c cell vector
stpipv        real      pressure, \({\cal P} \cdot {\cal V}\)
the next 2 entries - if NP:math:`_{n}`AT simulation is undertaken with iso > 0
h_z           real      MD cell height \(h_{z}\) to normal surface \({\cal A}\perp{z}\)
A\perpz       real      MD cell normal surface \({\cal A}\perp{z}={\cal V}/h_{z}\)
the next 2 entries - if a N:math:`gamma_{n}`AT simulation is undertaken with iso > 1
gamma_x       real      surface tension \(\gamma_{n_{x}}\) on normal surface \({\cal A}\perp{z}\)
gamma_y       real      surface tension \(\gamma_{n_{y}}\) on normal surface \({\cal A}\perp{z}\)

The LATS_E and LATS_I Files¶

These are formatted files containing electronic (LATS_E) and ionic (LATS_I)temperatures at user-requested intervals along the y-direction in the centre of the system’s xz-plane from two-temperature model calculations.

Each line in these files consists of a series of electronic or ionic temperatures along the y-direction – -eltsys(2)/2 $\le y \le$ +eltsys(2)/2 and -ntsys(2)/2 $\le y \le$ +ntsys(2)/2 at $x=z=0$ – corresponding to a requested timestep. The number of values in each line will depend on the number of electronic or ionic temperature cells requested by the user.

The PEAK_E and PEAK_I Files¶

These are formatted files containing statistics from two-temperature model calculations at user-requested intervals. Each line in these files corresponds to a requested time step and the data is based upon active coarse-grained electronic (CET) and ionic (CIT) temperature grid cells.

In the PEAK_E file, the data are formatted as follows:

record i
nstep       integer current MD time-step
time        real    elapsed simulation time
eltemp_min  real    minimum value of electronic temperature in system (K)
eltemp_max  real    maximum value of electronic temperature in system (K)
eltemp_mean real    mean value of electronic temperature in system (K)
eltemp_sum  real    sum of electronic temperatures in system (K)
Ue          real    total electronic energy in system (eV)

The PEAK_I file is formatted in a similar fashion, as follows:

record i
nstep         integer   current MD time-step
time          real      elapsed simulation time
tempion_min   real      minimum value of ionic temperature in system (K)
tempion_max   real      maximum value of ionic temperature in system (K)
tempion_mean  real      mean value of ionic temperature in system (K)
tempion_sum   real      sum of ionic temperatures in system (K)

The POPEVB Files¶

This is an unformatted file to print the weight of each chemical state $|\Psi^{(k)}_{\text{EVB}}\big|^{2}$ in the total EVB state, as described in section [sec:evb]. Values are printed at each time step only after equilibration. The structure of the printed data is as follows: Time (ps) $\,\,\,\,\,\,\,\,\,\,\,\,$ $|\Psi^{(1)}_{\text{EVB}}\big|^{2}$ $\,\,\,\,\,\,$ $|\Psi^{(2)}_{\text{EVB}}\big|^{2}$ $\,\,\,\,\,\,$ $|\Psi^{(3)}_{\text{EVB}}\big|^{2}$ $\cdots\cdots$ $|\Psi^{(N_F)}_{\text{EVB}}\big|^{2}$ where $N_F$ is the number of force-fields coupled via the EVB simulation.

The ICOORD, CCOORD and ADFDAT files¶

ICOORD and CCOORD are output files that log coordination number data for pairs of atomic species specified by the user. To perform this analysis and output these files the user must enter the keyword coord_calculate (see section The CONTROL File Directives) into the CONTROL file and crd (see section crd) into the FIELD file.

ICOORD is a dump file that can contain 2 types of data. The top of the file contains the initial coordination of each atom and the exact atoms it is coordinated to. There is an option to write this data at set intervals (the writing step interval) or just at the initial step. The bottom of the file provides the coordination distribution statistics for each atom after each writing step interval. The coordination distribution for the [atom list] - [atom list] pairs will also be displayed here.

CCOORD is a coordination displacement file that dumps the positions of all atoms that are considered to both change their initial local atomic coordination, and move more than a set distance from their initial position, at set intervals. This procedure is described in reference ²⁶.

ADFDAT is statistics file containing the angular distributions for the atom pairs specified.

The CURRENTS file¶

When currents are calculated a CURRENTS file will contain the values of density, transverse and longitudinal mometum currents, and energy currents for each time step (subject to stats_frequency), and each atom type. See sections Currents and The KPOINTS File.

The format will depend on the new CONTROL directive io_statis_yaml. See section Currents for an example of the YAML format.

For the plain text format the CURRENTS file will be formed of a series of blocks with the following structure

record 1:
t     real     simulation time (step*timestep)
type  a        1st atom type name
x1_r  real     1st kpoint's (real part) x component
x1_i  real     1st kpoint's (complex part) x component
y1_r  real     1st kpoint's (real part) y component
y1_i  real     1st kpoint's (complex part) y component
z1_r  real     1st kpoint's (real part) z component
z1_i  real     1st kpoint's (complex part) z component
...
zn_r  real     nth kpoint's (real part) z component
zn_i  real     nth kpoint's (complex part) z component
...
record l:
t     real     simulation time (step*timestep)
type  a        lth atom type name
x1_r  real     1st kpoint's (real part) x component
x1_i  real     1st kpoint's (complex part) x component
y1_r  real     1st kpoint's (real part) y component
y1_i  real     1st kpoint's (complex part) y component
z1_r  real     1st kpoint's (real part) z component
z1_i  real     1st kpoint's (complex part) z component
...
zn_r  real     nth kpoint's (real part) z component
zn_i  real     nth kpoint's (complex part) z component

By default for each time and atom type there will be three such records. The first being the density, the second the longitudinal momentum current, and the third the transverse momentum current. If energy_currents On is specified there will be a fourth record for energy currents.