Perple_X 07 Seismic Velocity
Calculations
!!!WARNING!!!
This tutorial is for
an out-of-date version (Perple_X
07), the current version (Perple_X
666) of the tutorial is at
seismic velocity tutorial.
Introduction
Thermodynamic data file preparation
A comment on
missing data (it's missing)
Computational
Algorithm for Seismic Velocities
A Worked Example
Running Build: problem setup
Running Vertex: phase diagram section
computation
Running Pssect: phase diagram section
depiction
Running Werami: extraction of
seismic velocities
Graphical Representation
Pscontor
Matlab Plotting
Figures:
Figure 1:
Perple_X program structure
Figure
2: Metabasalt phase relations
Figure
3: Metabasalt P-wave velocity
Seismic compressional and shear
wave velocities through rock are determined by: the corresponding velocities
within the constituent minerals; the amounts of the minerals; and rock texture.
For a rock in thermodynamic equilibrium, the first two factors are determined
entirely by thermodynamic properties and are computed automatically by Perple_X.
The third factor, texture, determines the relation of the bulk rock seismic
velocities to those of the constituent minerals. As texture is not a
thermodynamic property, the averaging schemes used to compute bulk rock
velocities are equivocal. In Perple_X,
Voigt-Reuss-Hill (VRH) averaging is used whereby the aggregate velocity is
computed from the average of the arithmetic and geometric means of the elastic
moduli of the individual phases
weighted by their volume fraction. The main advantage
of the VRH scheme, which has no theoretical basis, is that it does not depend on
texture. This averaging is done within the Perple_X
program WERAMI.
Recognition of the
thermodynamic constraints on seismic velocities has led some geophysicists to
use free energy minimization to compute mineral modes and compositions for
rocks. These modes and compositions are then used to estimate seismic velocities
from semi-empirical models. This approach is perhaps justified by the
uncertainties involved, but it is unquestionably thermodynamically inconsistent
in that it amounts to using one thermodynamic database to establish the amounts
of the minerals and another database to compute velocities. For geophysicists
who remain nonetheless enamored with empirical estimates of elastic modulii,
Perple_X can be used to make
calculations in this manner. However, I personally advocate using the same
thermodynamic data for the computation of both the stable mineralogy and seismic
velocities. The approach actually used by Perple_X
is determined by the structure of the data base as defined by the user and
discussed below.
Typical thermodynamic data tabulations
used for phase equilibrium calculations are designed for the
computation of isostatic phase equilibria (i.e., for systems without
differential
stresses), however seismic wave propagation involves both shear and
isostatic stresses. Therefore to compute seismic velocities with Perple_X
conventional thermodynamic data bases must be expanded to define the shear modulus (m),
which characterizes the thermodynamic response of each phase to shear stress.
This document describes the necessary modifications to
the thermodynamic data file and illustrates an application in which seismic
velocities are recovered from a phase equilibrium calculation.
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This section is
at:
http://www.perplex.ethz.ch/perplex_seismic_velocity_I.html
This section is
at:
http://www.perplex.ethz.ch/perplex_seismic_velocity_I.html
The example provided here (originally from
Connolly
& Kerrick 2002) illustrates the computation of absolute and relative seismic velocities through an altered metabasalt at p-T conditions relevant to
subduction zones at depths of 90-240 km. Relative velocities are, in this case,
the seismic velocities in the metabasalt divided by the corresponding velocities
in the ambient mantle, which is represented here by a pyrolite model
composition. The type of calculation required for this example is commonly
referred to as a phase diagram section or sometimes simply as a pseudosection.
The calculation
and interpretation of a phase diagram section consists of five steps (Figure
1): the problem
definition; the phase diagram section computation and depiction; computational
assessment; digital interpretation; and graphical interpretation. Each step
involves different programs and is described in the following sections:
Problem definition, BUILD
Phase diagram section computation, VERTEX
Pseudosection depiction, PSSECT
Digital interpretation, WERAMI
Graphical representation, PSCONTOR or MatLab
Figure 1. Perple_X program structure for gridded
minimization calculations (i.e., for phase diagram section and phase
fractionation calculations).
Running BUILD
The computation of relative
velocities requires the calculation of phase relations for both the metabasalt
of interest and the pyrolite mantle model. The BUILD dialog below details the
problem definition for the metabasalt, the slightly simpler dialog for the
pyrolite calculation is in the file dialog17b.txt.
The following script details
the prompts from the program BUILD (normal font) and user responses (bold
font). Explanatory comments are written in red.
Additional explanation on some prompts is available via the (help)
links.
c\jamie\Berple_X>build
NO is the
default ([cr]) answer to all Y/N prompts (help)
Enter name of
problem definition file to be created, <100 characters, left justified
[default = in]: (help)
in17a.dat
Enter thermodynamic data file name, left justified, [default = hp02ver.dat]:
(help)
The file
hp02ver.dat is a version of the Holland and Powell (1998, revised
2002) data base modified (Connolly 2005) to include shear modulii
relevant to the high pressure mineralogy of metabasalts. The hp02ver.dat file is
suitable for calculations to pressures approaching 12 GPa. The
sfo05ver.dat data base, which is primarily
from Stixrude & Lithgow-Bertelloni (2005, Khan et al. 2006), can be used
over the entire range of mantle conditions, but is for a simplistic chemical model (see
example #23).
hp02ver.dat
Enter the computational option file name, left justified, [default = perplex_option.dat]:
See: www.perplex.ethz.ch/perplex_options.html
Computational options used by Perple_X
can be controlled via the computational option file. This file is normally named
perplex_option.dat. Provision is made here to specify an alternative name
because it sometimes desirable to have customized option files for specific
purposes (e.g., high resolution or solvus calculations).
perplex_option.dat
The first
major block of prompts from BUILD determine the manner in which the chemical
components defined within the thermodynamic data file are to be used. VERTEX
permits components to be treated in four different ways: saturated phase
components are components whose chemical potentials are determined by the
(assumed) stability of a phase, most commonly a fluid, containing these
components; saturated components are components whose chemical potentials are
determined by the (assumed) stability of a pure phase(s) and or solutions
containing only the saturated-phase and saturated components; mobile components
are components whose chemical potentials are defined explicitly; and
thermodynamic components are components whose chemical potentials are the
dependent variables of a phase diagram calculation. Phase diagram calculations
require the specification of at least one thermodynamic component.
The current data base components are:
NA2O MGO
AL2O3 SIO2 K2O
CAO TIO2
MNO FEO
O2 H2O
CO2
Transform them (Y/N)? (help)
n
Calculations with a saturated phase (Y/N)?
(help)
The phase is: FLUID
Its compositional variable is: Y(CO2), X(O), etc.
Here the system is not assumed to be
saturated with respect to a fluid phase. With this closed system model fluid stability and composition is a function of the composition and
physical conditions. This model requires that the volatile components of
the fluid be specified as thermodynamic components as done below. There are
problems with such a model, but the closed system model for water-CO2
bearing systems is certainly less arbitrary (and probably more realistic) than
the petrological artifice of assuming that the system is saturated with respect
to a fluid with a fixed composition. More realistic models for devolatilization
require path-dependent models, such models can be implemented in Perple_X
in “phase fractionation
calculation” mode (and for phase fractionation with mass transfer see
Connolly 2005). The main problem with the closed system model is that it
implies that fluid generated by devolatilization remains within the system.
This problem can be overcome by instructing WERAMI to compute the seismic
properties of the solid aggregate (a limiting case).
n
Calculations with saturated components (Y/N)? (help)
n
Use
chemical potentials, activities or fugacities as independent variables (Y/N)?
(help)
n
Select
thermodynamic components from the set: (help)
NA2O
MGO AL2O3 SIO2
K2O CAO
TIO2 MNO
FEO O2
H2O CO2
Enter
names, left justified, 1 per line, [cr] to finish:
SIO2
TIO2
AL2O3
FEO
MGO
CAO
NA2O
K2O
H2O
CO2
**warning
ver016** you are going to treat a saturated (fluid) phase component as a
thermodynamic component, this may not be what you want to do. (help)
Select fluid equation of state: (help)
0 - X(CO2) Modified
Redlich-Kwong (MRK/DeSantis/Holloway)
1 - X(CO2) Kerrick & Jacobs 1981
(HSMRK)
2 - X(CO2) Hybrid MRK/HSMRK
3 - X(CO2) Saxena & Fei 1987
pseudo-virial expansion
4 - Bottinga &Richet 1981 (CO2
RK)
5 - X(CO2) Holland &Powell 1991,
1998 (CORK)
6 - X(CO2) Hybrid Haar et al
1979/CORK (TRKMRK)
7 - f(O2/CO2)-f(S2) Graphite
buffered COHS MRK fluid
8 - f(O2/CO2)-f(S2) Graphite
buffered COHS hybrid-EoS fluid
9 - Max X(H2O) GCOH fluid Cesare
& Connolly 1993
10 - X(O) GCOH-fluid hybrid-EoS
Connolly & Cesare 1993
11 - X(O) GCOH-fluid MRK Connolly
& Cesare 1993
12 - X(O)-f(S2) GCOHS-fluid hybrid-EoS
Connolly & Cesare 1993
13 - X(H2) H2-H2O hybrid-EoS
14 - EoS Birch & Feeblebop (1993)
15 - X(H2) low T H2-H2O hybrid-EoS
16 - X(O) H-O HSMRK/MRK hybrid-EoS
17 - X(O) H-O-S HSMRK/MRK hybrid-EoS
18 - X(CO2) Delany/HSMRK/MRK hybrid-EoS,
for P >10 kb
19 - X(O)-X(S) COHS hybrid-EoS
Connolly & Cesare 1993
20 - X(O)-X(C) COHS hybrid-EoS
Connolly & Cesare 1993
21 - X(CO2) Halbach &Chatterjee 1982,
P >10 kb, hybrid-Eos
22 - X(CO2) DHCORK, hybrid-Eos
23 - Toop-Samis Silicate Melt
24 -
f(O2/CO2)-N/C Graphite saturated COHN MRK fluid
25 - H2O-CO2-NaCl Aranovich & Haefner 2004
5
The second
major block of prompts defines the explicit computational variables.
Specify computational mode: (help)
1 -
Unconstrained minimization
2 - Constrained minimization on a 2d grid [default]
3 - Constrained minimization on a 1d grid
4 - Output pseudocompound data
5 - Phase fractionation calculations
Unconstrained optimization should be used for the calculation of composition,
mixed variable, and Schreinemakers diagrams. Gridded minimization can be used to
construct one- and two-dimensional phase diagram sections.
2
Here we
are concerned with a normal P-T section; however, in gridded minimization
it is possible to construct sections as a function of any
arbitrarily defined composition (variable X(C1) in this prompt) or along a
geothermal gradient, for examples of such calculations refer to the
T-X, P-X and X-X section and
phase abundances
along an abritary path tutorials.
The data
base has P(bars) and T(K) as default independent potentials. Make one dependent
on the other, e.g., as along a geothermal gradient (y/n)? (help)
n
Select x-axis variable: (help)
1 - P(bars)
2 - T(K)
3 - Composition
X(C1)* (user defined)
*X(C1) can not be selected as the y-axis variable
2
Enter
minimum and maximum values, respectively, for: T(K)
673
1473
Enter
minimum and maximum values, respectively, for: P(bars)
30000
80000
The
following blurb provides information on the resolution with which phase
relations are mapped as a function of the section variables. This resolution is
controlled via the
grid_parameters keywords specified in the perplex_option.dat file. When the auto_refine option
is set on (the default) calculations are done in two iterations: an initial low quality
"exploratory stage" is used to establish the range of phase compositions; and a
second high resolution "auto-refine stage" to refine the final results. The two
stages are executed in a single calculation if the auto_refine keyword is set to
"auto".
For gridded
minimization, grid resolution is determined by the number of levels (grid_levels)
and the resolution at the lowest level in the X- and Y-directions (x_nodes and
y_nodes) these parameters are currently set for the exploratory and autorefine
cycles as follows:
stage grid_levels xnodes ynodes effective resolution
exploratory 1 20 20 20 x 20 nodes
auto-refine 4 60 60 473 x 473 nodes
To change these
options edit or create the file perplex_option.dat
See: www.perplex.ethz.ch/perplex_options.html
Specify component amounts by weight (Y/N)?
y
Enter weight amounts of the components: (help)
SIO2 TIO2 AL2O3 FEO MGO CAO NA2O K2O H2O CO2
for the bulk composition of interest:
45 1.1 15.26 9.84 6.54 12.66 2.03 0.55 2.63 2.9
The next
block of prompts define the output required by the user.
Do
you want a print file (Y/N)?
n
Enter the
plot file name, <100 characters, left justified [default = pl]: (help)
plot17a
The final block
of prompts from BUILD define the phases for the calculation.
Exclude phases (Y/N)? (help)
y
Here, experience leads me to make four exclusions: Clinozoisite (cz) is excluded to suppress the zoisite-clinozoisite transition,
which is primarily a distraction in terms of interpreting phase equilibria. The
water endmember of the Holland & Powell melt model (h2oL), is excluded because
the endmember is (incorrectly) more stable than water at high pressure and low
temperature. The "aluminum-free chlorite" endmember (afchl) of the Baker,
Holland & Powell chlorite model is excluded because the use of this endmember
requires many more pseudocompounds to resolve chlorite compositions yet it has
almost no effect on the computed phase relations. The ordered-dolomite (odo)
endmember required for Holland & Powell's (2004) dolomite model is excluded
because the model, of dubious value in any case, is not employed here.
Do you want to be prompted for phases (Y/N)?
n
Enter names, left justified, 1 per line, [cr] to finish:
cz
afchl
h2oL
odo
Do you want to treat solution phases (Y/N)?
y
Enter solution model file name [default = solut_07.dat]
left justified, <100 characters: (help)
solut_07.dat
...diagnostics omitted...
BUILD reads
the solution model file and determines which solutions are consistent with the
specified problem. The diagnostics (omitted here) can usually
be ignored. They are useful if you discover that a solution you wish to include
is not present in the list of solutions BUILD offers.
Select phases from the following list, enter 1 per line, left
justified, [cr] to finish: (help)
Bio(HP) TiBio(WPH) TiBio(HP) Chl(HP) O(SG) E(SG)
Omph(HP) melt(HP) pMELTS(G) Pheng(HP) Sapp(HP) Sapp(KWP)
Osm(HP) GaHcSp F F(salt) T St(HP)
Ctd(HP) Carp hCrd Sud(Livi) Sud Cumm
Anth Gl Tr TrTsPg(HP) GlTrTs GlTrTsPg
Amph(DHP) Amph(DPW) feldspar Pl(h) Kf San
MaPa KN-Phen MuPa Mica(CH)
Bio(TCC) O(HP)
Cpx(l) Cpx(h) Mont Do(HP) M(HP) Do(AE)
Cc(AE) Sp(JR) Sp(GS) Sp(HP) IlGkPy Neph(FB)
GrPyAlSp(B GrPyAlSp(G Gt(HP) Gt(EWHP) Gt(WPH) A-phase
Chum Atg B P Qpx Mn-Opx
OrFsp(C1) AbFsp(C1) Pl(I1,HP) Fsp(C1) oCcM(HP) O(stx)
Sp(stx) Gt(stx) Opx(stx) Cpx(stx) o-Amph cOmph(HP)
CrGt CrOpx(HP) Opx(HP) Cpx(HP) CrSp Ca-Amph(D)
Na-Amph(D)
F
Chl(HP)
Mica(CH)
San
Pl(h)
Gt(HP)
Do(HP)
M(HP)
Opx(HP)
Amph(DPW)
Omph(HP)
Bio(TCC)
T
Because fluid
is not specified as a saturated phase it is necessary to
specify explicitly that a fluid solution may be present (i.e., the solution
model F).
Enter calculation title:
staudigel closed system model
Top
If the auto_refine
option is on calculations are done in two stages: an initial low quality
exploratory stage establishes the range of phase compositions; and a final high
resolution auto-refine stage. These stages are executed in a single calculation,
as done here, only if the value of the auto_refine
keyword is auto.
Before running VERTEX be sure to
verify that the auto_refine
keyword is set to auto in your copy of perplex_option.dat.
c\jamie\Berple_X>
vertex
VERTEX begins
by echoing the current settings for computational options, these are either the
defaults or the values specified in
perplex_option.dat.
Perple_X options
are currently set as:
Keyword:
Value: Permitted values [default]:
dependent_potentials off
off [on ]
bad_number
0. [0.0]
solvus_tolerance 0.050
0->1 [0.05], 0 => p=c pseudocompounds, 1 => homogenize
zero_mode
0.1E-05 0->1 [1e-6], < 0 => off
zero_bulk
0.1E-05 0->1 [1e-6], < 0 => off
adaptive optimization
iteration limit
4 >0 [3], value 1 of iteration
keyword
refinement factor 3
>2*r [5], value 2 of iteration keyword
refinement points 10
0->100 [10], value 3 of iteration keyword
initial_resolution 0.10
0->1 [0.1], 0 => off
stretch_factor
0.016 >0 [0.0164]
reach_factor
0.9 >0.5 [0.9]
subdivision_override off
[off] lin str
auto_refine
aut off [manual] auto
auto_refine_factor_I 3
>=1 [3]
auto_refine_factor_II 5
>=1 [10]
auto_refine_factor_III 2
>=1 [3]
auto_refine_slop 0.010
[0.01]
hard_limits
off [off] on
T_stop (K)
0.0 [0]
Gridded minimization parameters:
x_nodes
20 / 60 [20/40], >0, <2048; effective x-resolution
20 / 473 nodes
y_nodes
20 / 60 [20/40], >0, <2048; effective y-resolution
20 / 473 nodes
grid_levels
1 / 4 [1/4], >0, <10
1d_path
10 /150 [20/150], >0, <2048
Parameters for Schreinemakers and Mixed-variable diagram
calculations:
variance
1 /99 [1/99], >0, maximum true variance
increment
0.100 /0.025 [0.1/0.025], default search/trace variable increment
efficiency
3 [3] >0 < 6
reaction_format min
[min] full stoichiometry S+V everything
reaction_list
off [off] on
console_messages on
[on] off
short_print_file on
[on] off
WERAMI/MEEMUM output options:
compositions
mol wt [mol]
proportions
vol wt [vol] mol
interpolation
on off [on ]
extrapolation
off on [off]
vrh_weighting
0.5 0->1 [0.5]
cumulative_modes
off [off] on
Worst case (Cartesian) compositional resolution (mol %)
Stage Adaptive
Non-Adaptive* Non-Adaptive**
Exploratory 0.146
10.000 10.000
Auto-refine 0.049
2.000 5.000
* - composition/mixed variable diagrams, ** - Schreinemakers diagrams
To change these options edit or create the file perplex_option.dat
See: www.perplex.ethz.ch/perplex_options.html
VERTEX then
requests the problem definition
file created by BUILD (in17a.dat):
Enter problem definition file name (i.e. the file created with
BUILD), left justified:
in17a.dat
and lists
the input/output files to be used/created for the calculation. Several output
files are created in addition to the plot file "plot17a" requested by the user,
among these are: "bplot17a" named by adding the
prefix "b" to the plot file name,
"pseudocompound_glossary.dat", and "auto_refine_in17a.dat.txt".
The files
pseudocompound_glossary.dat and auto_refine_in17a.dat.txt
(named by appending the name of the problem definition file to the prefix "auto_refine_"
and adding the suffix ".txt") contain information about the range of
compositions considered in the calculation. In addition to the auto_refine text
file, VERTEX generates a less user friendly version of the same data in
"auto_refine_in17a.dat" (named by appending the problem definition file name
to the prefix "auto_refine_"), which is used by
VERTEX in the auto-refine stage.
It is only necessary to be aware of these files if you wish to store or analyze
results in a different directory than the working directory for VERTEX.
Reading thermodynamic data from file: hp02ver.dat
Writing print output to file: none requested
Writing plot output to file: plot17a
Writing pseudocompound glossary to file: pseudocompound_glossary.dat
Reading solution models from file: solut_07.dat
Writing bulk composition plot output to file: bplot17a
Writing data for auto-refinement to file: auto_refine_in17a.dat.txt
All "make
definitions" consistent with the problem definition file are output next. Make
definitions define thermodynamic entities (e.g., buffers, endmembers or
reactions) as a linear combination of independent entries in the thermodynamic
data file. The make definitions are in the header section of the thermodynamic
data file (hp02ver.dat)
and can be modified, deleted or created for your own purposes.
Summary of valid make definitions:
MGO AL2O3 SIO2 K2O TIO2 FEO H2O
tbi 1.00 0.50 1.00 0.50 1.00 0.00 1.00
tbi1 2.00 0.50 3.00 0.50 1.00 0.00 0.00
fbr 0.00 0.00 0.00 0.00 0.00 1.00 1.00
fchum 0.00 0.00 4.00 0.00 0.00 9.00 1.00
fphA 0.00 0.00 2.00 0.00 0.00 7.00 3.00
fper 0.00 0.00 0.00 0.00 0.00 1.00 0.00
fatg 0.00 0.00 34.00 0.00 0.00 48.00 31.00
sil8L 0.00 1.60 1.60 0.00 0.00 0.00 0.00
fo8L 4.00 0.00 2.00 0.00 0.00 0.00 0.00
fa8L 0.00 0.00 2.00 0.00 0.00 4.00 0.00
q8L 0.00 0.00 4.00 0.00 0.00 0.00 0.00
The remaining
section of the initial console output (abridged below) consists of
information and warnings on the solution models to be used in the calculation.
These messages inform the user as to which solution models in the solution model
file are compatible with the problem definition, i.e., that the solution
end-members are possible phases for the calculation. If only a subset of the
solution model end-members are present, the messages indicate how the model will
be reformulated in terms of
this subset. If you do not get the solution models you requested, or if you get
different solution compositions than you expect, these messages may be helpful.
The diagnostics also indicate the number of static pseudocompounds used for each
solution, this number is useful for determining which solution models are costly
in terms of computer memory.
**warning ver114** the following endmembers are missing for Bio(TCC)
ffbi_i fbi
**warning ver050** reformulating reciprocal solution: Bio(TCC) because of
missing endmembers.(reformulation can be controlled explicitly by excluding
additional endmembers).
338 pseudocompounds generated for: Bio(TCC)
**warning ver114** the following endmembers are missing for Chl(HP)
mame_i mafchl_i mnchl
fafchl_i afchl
**warning ver050** reformulating reciprocal solution: Chl(HP)
because of missing endmembers. (reformulation can be controlled explicitly by
excluding additional endmembers).
118 pseudocompounds generated for: Chl(HP)
63 pseudocompounds generated for: Omph(HP)
9 pseudocompounds generated for: F
118 pseudocompounds generated for: T
**warning ver114** the following endmembers are missing for Amph(DPW)
mfets ffets_i
**warning ver050** reformulating reciprocal solution: Amph(DPW) because
of missing endmembers. (reformulation can be controlled explicitly by
excluding additional endmembers).
3141 pseudocompounds generated for: Amph(DPW)
9 pseudocompounds generated for: Pl(h)
9 pseudocompounds generated for: San
4288 pseudocompounds generated for: Mica(CH)
9 pseudocompounds generated for: Do(HP)
**warning ver114** the following endmembers are missing for M(HP)
rhc
9 pseudocompounds generated for: M(HP)
**warning ver114** the following endmembers are missing for Gt(HP)
spss
63 pseudocompounds generated for: Gt(HP)
118 pseudocompounds generated for: Opx(HP)
Total number of pseudocompounds: 8292
** Starting exploratory computational stage **
The preceding
line terminates the initial section of the console output. Often this section is
followed by warning messages such as:
**warning
ver369** failed to converge at T= 673.00 K, P= 72105.3 bar Using Murnaghan EoS,
probably for Ghiorso et al. MELTS/PMELTS endmember data. Volume estimated using
3rd order Taylor series.
that indicate
unstable numerical behavior of specialized equations of state, most commonly
these result because the calibration is being used beyond the range of physical
conditions for which it was intended. In general, these warnings have no
significant consequences, but if you have doubts it is possible to eliminate the
offending entity (e.g., here endmembers of the pMELTS(G) silicate melt model are
causing problems at subsolidus temperatures and pressures far beyond the 4 GPa
upper limit for the pMELTS calibration).
During the
computation VERTEX outputs progress information:
5.0%
done with low level grid.
10.0% done with low level grid.
15.0% done with low level grid.
...
85.0% done with low level grid.
90.0% done with low level grid.
95.0% done with low level grid.
100.0% done with low level grid.
Beginning grid refinement stage.
After
completion of the exploratory stage, VERTEX indicates which solution phases were not stable
and the compositional ranges of the stable solution phases, this information is
echoed in the
"auto_refine_in17a.dat.txt" file and is
used to increase for the subsequent auto-refine stage.
WARNING: The following solutions were input, but are not stable:
Bio(TCC)
Chl(HP)
Amph(DPW)
Pl(h)
Opx(HP)
Endmember compositional ranges for model: Omph(HP)
Endmember Minimum Maximum
di
0.40153 0.82889
jd
0.07778 0.52822
Endmember compositional ranges for model: F
Endmember Minimum Maximum
CO2
0.00000 0.33032
Site fraction ranges for multisite model: T
Site 1
Species Minimum Maximum
1
0.91556 0.94222
Site 2
Species Minimum Maximum
1
0.99444 0.99889
...output
abridged...
At this point
if the auto_refine keyword were set to manual (i.e., "man"), VERTEX would
terminate, allowing the user to examine intermediate results, but requiring that
VERTEX be run a second time to obtain the final high resolution calculation.
However this example has been run with auto_refine set to auto (i.e., "aut"),
thus the VERTEX automatically begins the auto-refine stage of the calculation:
Reading
auto-refinement data from file: auto_refine_in17a.dat
At the
beginning of auto-refine stage VERTEX eliminates all solution phases
specified in the problem definition file (in17a.dat) that were not stable in the
exploratory calculation and then restricts the compositional ranges for the
remaining solutions to those found in the exploratory calculation (plus an
increment [auto_refine_slop]
to allow for inaccuracy), additionally the compositional resolution of the
calculation in these restricted
compositional resolution
is increased by the
auto_refine_factor.
Eliminating
solution model: Chl(HP) in auto-refinement.
Eliminating
solution model: Pl(h) in auto-refinement.
Eliminating
solution model: Opx(HP) in auto-refinement.
Eliminating
solution model: Amph(DPW) in auto-refinement.
Eliminating
solution model: Bio(TCC) in auto-refinement.
148 pseudocompounds generated for: Omph(HP)
11 pseudocompounds generated for: F
2 pseudocompounds generated for: T
31 pseudocompounds generated for: San
164205 pseudocompounds generated for: Mica(CH)
4 pseudocompounds generated for: Do(HP)
14 pseudocompounds generated for: M(HP)
117 pseudocompounds generated for: Gt(HP)
Total number of pseudocompounds: 164532
** Starting auto_refine computational stage **
During
auto-refinement VERTEX
may write diagnostics such as:
WARNING:
composition of solution Do(HP) has reached an internal limit (0.759) on site 1
for species 1.
If this warning
occurs during auto-refinement, the problem can be circumvented by increasing the
auto_refine_slop specified in perplex_option.dat.
For the
remainder of this calculation the internal limit has been relaxed to: 0.726
that commonly indicates that the composition of a phase
has exceeded the range discovered in a previous exploratory stage. When this occurs VERTEX relaxes the range as indicated,
which usually prevents any significant consequences. If this diagnostic occurs during
the exploratory stage itself it may have more serious consequences. In this
case, it is wise to widen the relevant limits specified in the solution model
file.
...
98.3% done
with low level grid.
100.0% done with
low level grid.
In contrast to
the exploratory stage, the grid_parameter keyword specifies a multi-level (i.e., 4-level) grid
for the auto-refine stage, thus
after the calculation of the first (or "low level") grid, VERTEX makes three
refinements of the grid, each of these refinements takes roughly twice the
time of the previous refinement.
Beginning grid
refinement stage.
649
grid cells to be refined at grid level 2
...working ( 501 minimizations done)
...working ( 1003 minimizations done)
refinement at level 2 involved 1376 minimizations
4976
minimizations required of the theoretical limit of 14161
1202 grid
cells to be refined at grid level 3
...working ( 128 minimizations done)
...working ( 629 minimizations done)
...working ( 1131 minimizations done)
...working ( 1634 minimizations done)
...
VERTEX terminates as in the
exploratory cycle with a summary of the phase compositions and writes a new
auto-refine data file.
Top
Running
PSSECT
PSSECT
generates PostScript graphical output and can be used once the phase diagram section has been calculated with VERTEX. The default
plot from PSSECT shows the computed phase relations (Figure 3) and is
generated by the following dialog.
c\jamie\Berple_X>
pssect
...
Enter problem
definition file name (i.e. the file created with BUILD), left justified:
in17a.dat
PostScript will be written to file:
plot17a.ps
Answer yes to
the following prompt to modify features such as axis labeling, size, and shape.
Modify the default plot (y/n)?
n
Figure 2 Computed metabasalt phase relations (plot17a.ps), this figure differs from Figure 2a of Connolly & Kerrick (2002) because the published figure was calculated
with different solution models.
Top
WERAMI permits the user to extract
information from a phase diagram section at a point, throughout a region, or along a
line or curve. The latter two options generate output that can be plotted with
programs PSCONTOR or PSPTS or imported into general-purpose programs such as
Matlab. The dialog and output for each of these modes is detailed in the
pseudosection tutorial. Here the second mode is used to extract
P-wave velocities for the metabasalt over the entire range of
pressure-temperature conditions represented by the phase diagram section.
c\jamie\Berple_X> werami
Enter problem definition file name (i.e. the file created with BUILD), left justified:
in17a.dat
Select operational mode:
1 - compute properties at specified conditions
2 - create a property grid (plot with pscontor)
3 - compute properties along a curve or line (plot with pspts)
4 - as in 3, but input from file
0 - EXIT
2
Select a property:
1 - Specific enthalpy (J/m3)
2 - Density (kg/m3)
3 - Specific Heat capacity (J/K/m3)
4 - Expansivity (1/K, for volume)
5 - Compressibility (1/bar, for volume)
6 - Weight percent of a component
7 - Mode (Vol %) of a compound or solution
8 - Composition of a solution
9 - Grueneisen thermal ratio
10 - Adiabatic bulk modulus
11 - Shear modulus (bar)
12 - Sound velocity (km/s)
13 - P-wave velocity (Vp, km/s)
14 - S-wave velocity (Vs, km/s)
15 - Vp/Vs
16 - Specific Entropy (J/K/m3)
17 - Entropy (J/K/kg)
18 - Enthalpy (J/kg)
19 - Heat Capacity (J/K/kg)
20 - Specific mass of a phase (kg/m3-solid)
21 - Poisson ratio
22 - Molar Volume (J/bar)
23 - Chemical potentials (J/mol)
24 - Assemblage Index
25 - Modes of all phases
13
Calculate individual phase properties (y/n)?
n
Include fluid in computation of aggregate (or modal) properties (y/n)?
n
Change default variable range (y/n)?
n
Enter number of nodes in and x and y directions: (help)
100 100
Writing grid data to file: cplot17a
**warning ver637** Immiscibility occurs in one or
more phases interpolation will be turned off at all affected nodes. To overide
this feature at the risk of computing inconsistent properties turn solvus
testing off in perplex_option.dat
Range of >0 data is: 7.90399 -> 8.88201
Evaluate additional properties (y/n)?
n
Select operational mode:
1 - compute properties at specified conditions
2 - create a property grid (plot with pscontor)
3 - compute properties along a curve or line (plot with pspts)
4 - as in 3, but input from file
0 - EXIT
0
The structure of the grid data file is described in README WERAMI GRID FORMAT.
Top
Grid data generated by WERAMI can be plotted by various commercial packages such
as MatLab or Maple, alternatively (the relatively crude) Perple_X
program PSCONTOR can be used to generate an interpreted PostScript plot. Both
possibilities are demonstrated here.
c\jamie\Berple_X>pscontor
Enter the
CONTOUR plot file name:
cplot17a
PostScript
will be written to file:
cplot17a.ps
Reset plot
limits (y/n)?
n
Modify
default drafting options (y/n)?
answer yes to modify:
- picture transformation
- x-y plotting limits
- relative lengths of axes
- text label font size
- line thickness
- curve smoothing
- axes labeling and gridding
y
Modify
default picture transformation (y/n)?
n
Modify
ratio of x to y axis length (y/n)
n
Modify
default text scaling (y/n)?
n
Use
minimum width lines (y/n)?
n
Fit curves
with B-splines (y/n)?
y
Contoured
variable range: 7.940270 ->8.953970
Modify default contour interval (y/n)?
y
Enter min,
max and interval for contours:
7.95 8.95 0.05
Modify default axes (y/n)?
y
Enter the
starting value and interval for major tick marks on
the
X-axis (current values are: 673.0 160.0)
Enter new values:
673 160
Enter the
starting value and interval for major tick marks on
the
Y-axis (current values are: 0.300E+05 0.100E+05)
Enter new values:
30000 10000
Cancel half interval tick marks (y/n)?
n
Draw tenth
interval tick marks (y/n)?
n
Rescale
axes text (y/n)?
n
Turn
gridding on (y/n)?
n
The output (Figure
4) from PSCONTOR can be printed on any PostScript printer or viewed on a
Postscript viewer such as Ghostview. Alternatively, the postscript plot may be
imported into graphical editors such as Adobe Illustrator or Coreldraw. PSCONTOR
does not label the plotted contours, but it does use a heavy solid line for the
minimum contour and a heavy broken line to indicate the maximum contour value.
If this information is not sufficient to determine the contour values, WERAMI
can be used in mode 1 to query the value of the property of interest at any
point within the phase diagram section.
MatLab
Plotting
The grid data file generated by
WERAMI (README
WERAMI GRID FORMAT) can be imported into MatLab or other commercial plotting
routines. Three MatLab plotting scripts (Perple_X_#.#.#_MatLab_scripts.zip)
are provided with Perple_X to allow
users to view grid data quickly:
surface_plot.m
- plot a 3D image of the data
automatically_labeled_contour_plot.m
- 2D contour plot, contours chosen and labeled by Matlab
manually_labeled_contour_plot.m
- 2D contour plot, contours chosen and labeled by user
ratio_contour_plot_manually_labeled.m - 2D contour plot of the ratio of
properties in two different
WERAMI plot files (e.g., density ratio of two rocks)
Examples of the first and third
plots are shown in
Figure 4. Users unfamiliar with MatLab should be aware that MatLab expects the user to interactively label the contours generated by
the third script by "clicking" on the contours, once the user has
finished she must terminate the interactive labeling mode by pressing enter.
To make a MatLab plot, the user must
start MatLab and change directory to the directory containing the Perple_X
plotting scripts and then type the name of the desired script (without the “.m”
suffix), e.g., “surface_plot”, the rest is self-explanatory.
Figure 3:
Three plot variations of the computed metabasalt P-wave velocities (km/s). The
uppermost plot is an interactively labeled contour plot generated in MATLAB by
the script manually_labeled_contour_plot. The middle plot is a false colour
image also generated with surface_plot.m, but with the lighting changed from
“phong” to “giraud”. The lowermost plot is the plot generated by PSCONTOR.
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