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bobmyhillbobmyhill
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allow splitting of perplex calculations over multiple files
1 parent 3ca02be commit f6071ec

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2 files changed

+168
-46
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2 files changed

+168
-46
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‎contrib/perplex/create_lo_res_table.py‎

Lines changed: 146 additions & 42 deletions
Original file line numberDiff line numberDiff line change
@@ -6,18 +6,72 @@
66
from perplex_utils import run_vertex, run_pssect
77
from perplex_utils import create_perplex_table
88

9+
10+
def create_table(
11+
perplex_bindir,
12+
project_name,
13+
database,
14+
perplex_option_file,
15+
composition,
16+
pressure_range,
17+
temperature_range,
18+
n_pressures,
19+
n_temperatures,
20+
outfile,
21+
):
22+
# Make the build file
23+
# This file contains the information about the project, such as the
24+
# composition, the database, and the options for Perple_X.
25+
print("* Making build file...")
26+
make_build_file(
27+
perplex_bindir,
28+
project_name,
29+
database,
30+
perplex_option_file,
31+
composition,
32+
pressure_range,
33+
temperature_range,
34+
verbose=False,
35+
)
36+
37+
# Run the Perple_X vertex command to do the Gibbs minimization
38+
# and create output files containing the equilibrium assemblages.
39+
print("* Running vertex...")
40+
run_vertex(perplex_bindir, project_name, verbose=False)
41+
42+
# Run the Perple_X pssect command to create a postscript
43+
# file containing the phase diagram.
44+
print("* Running pssect...")
45+
run_pssect(perplex_bindir, project_name, convert_to_pdf=False, verbose=False)
46+
47+
# Create the BurnMan-readable table from the vertex output
48+
print("* Creating BurnMan-readable table...")
49+
create_perplex_table(
50+
perplex_bindir,
51+
project_name,
52+
outfile,
53+
n_pressures,
54+
n_temperatures,
55+
pressure_range,
56+
temperature_range,
57+
)
58+
59+
960
if __name__ == "__main__":
1061
# Define the project parameters
1162
project_name = "iron_olivine_lo_res"
1263
database = databases["stx24"]
1364
composition = burnman.Composition(
1465
{"MgO": 1.8, "FeO": 0.2, "SiO2": 1.0, "Fe": 0.1}, "molar"
1566
)
16-
pressure_range = [1.0e5, 10.0e9]
17-
temperature_range = [200.0, 3000.0]
18-
n_pressures = 11
19-
n_temperatures = 15
20-
outfile = "iron_olivine_lo_res_table.dat"
67+
pressure_range_total = [1.0e5, 10.0e9]
68+
temperature_range_total = [200.0, 3000.0]
69+
n_pressures_per_split = 6
70+
n_temperatures_per_split = 8
71+
n_splits_pressure = 2
72+
n_splits_temperature = 2
73+
74+
outfile_base = "iron_olivine_lo_res_table"
2175

2276
perplex_dir = os.path.join(os.getcwd(), "perplex-installer/Perple_X")
2377
perplex_bindir = os.path.join(os.getcwd(), "perplex-installer/Perple_X/bin")
@@ -50,8 +104,8 @@
50104
# In the refinement stage, the number of nodes is increased.
51105
# Any solutions not present on any of the bounding nodes will be excluded
52106
# from the calculations.
53-
n_P_exploratory = int((n_pressures + 1) / 2)
54-
n_T_exploratory = int((n_temperatures + 1) / 2)
107+
n_P_exploratory = int((n_pressures_per_split + 1) / 2)
108+
n_T_exploratory = int((n_temperatures_per_split + 1) / 2)
55109

56110
# Create the Perple_X options file
57111
with open(perplex_option_file, "w") as f:
@@ -61,46 +115,96 @@
61115
f.write("auto_refine auto\n") # Automatically refine the grid
62116
f.write("grid_levels 1 1\n") # Do not use adaptive grid refinement
63117
f.write(
64-
f"x_nodes {n_P_exploratory} {n_pressures}\n"
118+
f"x_nodes {n_P_exploratory} {n_pressures_per_split}\n"
65119
) # Exploratory and final number of pressure nodes
66120
f.write(
67-
f"y_nodes {n_T_exploratory} {n_temperatures}\n"
121+
f"y_nodes {n_T_exploratory} {n_temperatures_per_split}\n"
68122
) # Exploratory and final number of temperature nodes
69123

70-
# Make the build file
71-
# This file contains the information about the project, such as the
72-
# composition, the database, and the options for Perple_X.
73-
print("Making build file...")
74-
make_build_file(
75-
perplex_bindir,
76-
project_name,
77-
database,
78-
perplex_option_file,
79-
composition,
80-
pressure_range,
81-
temperature_range,
82-
verbose=False,
83-
)
124+
# Create the table(s) using the defined parameters
125+
delta_P = (pressure_range_total[1] - pressure_range_total[0]) / n_splits_pressure
126+
delta_T = (
127+
temperature_range_total[1] - temperature_range_total[0]
128+
) / n_splits_temperature
84129

85-
# Run the Perple_X vertex command to do the Gibbs minimization
86-
# and create output files containing the equilibrium assemblages.
87-
print("Running vertex...")
88-
run_vertex(perplex_bindir, project_name, verbose=False)
130+
for i_P in range(n_splits_pressure):
131+
for i_T in range(n_splits_temperature):
132+
pressure_range = [
133+
pressure_range_total[0] + i_P * delta_P,
134+
pressure_range_total[0] + (i_P + 1) * delta_P,
135+
]
136+
temperature_range = [
137+
temperature_range_total[0] + i_T * delta_T,
138+
temperature_range_total[0] + (i_T + 1) * delta_T,
139+
]
140+
if n_splits_pressure > 1 or n_splits_temperature > 1:
141+
outfile = f"{outfile_base}_P{i_P + 1:02d}_T{i_T + 1:02d}.dat"
142+
else:
143+
outfile = f"{outfile_base}.dat"
89144

90-
# Run the Perple_X pssect command to create a postscript
91-
# file containing the phase diagram.
92-
print("Running pssect...")
93-
run_pssect(perplex_bindir, project_name, convert_to_pdf=False, verbose=False)
145+
print(
146+
f"Creating table [{i_P + 1}/{n_splits_pressure}, {i_T + 1}/{n_splits_temperature}]"
147+
)
148+
# Create the table for the current split
149+
create_table(
150+
perplex_bindir,
151+
project_name,
152+
database,
153+
perplex_option_file,
154+
composition,
155+
pressure_range,
156+
temperature_range,
157+
n_pressures_per_split,
158+
n_temperatures_per_split,
159+
outfile,
160+
)
161+
162+
# If there are splits, merge the output files into one
163+
if n_splits_pressure > 1 or n_splits_temperature > 1:
164+
print("Merging output files...")
165+
166+
# Read the header lines from the first split file
167+
first_split_outfile = f"{outfile_base}_P01_T01.dat"
168+
with open(first_split_outfile, "r") as infile:
169+
header_lines = [next(infile) for _ in range(13)]
170+
171+
total_n_pressures = (n_pressures_per_split - 1) * n_splits_pressure + 1
172+
total_n_temperatures = (n_temperatures_per_split - 1) * n_splits_temperature + 1
173+
header_lines[6] = f" {total_n_pressures}\n"
174+
header_lines[10] = f" {total_n_temperatures}\n"
175+
176+
# Load all other lines from the split files into a single list of lists
177+
all_lines = []
178+
for i_P in range(n_splits_pressure):
179+
for i_T in range(n_splits_temperature):
180+
split_outfile = f"{outfile_base}_P{i_P + 1:02d}_T{i_T + 1:02d}.dat"
181+
with open(split_outfile, "r") as infile:
182+
lines = infile.readlines()[13:]
183+
all_lines.extend(lines)
184+
185+
# Sort the lines by pressure and temperature, looping over pressures first
186+
all_lines.sort(key=lambda x: (float(x.split()[1]), float(x.split()[0])))
187+
188+
# Remove duplicate pressures and temperatures from the sorted list
189+
unique_lines = []
190+
seen = set()
191+
for line in all_lines:
192+
pressure_temp = (float(line.split()[0]), float(line.split()[1]))
193+
if pressure_temp not in seen:
194+
seen.add(pressure_temp)
195+
unique_lines.append(line)
196+
197+
# Check the total number of unique lines is as expected
198+
if len(unique_lines) != total_n_pressures * total_n_temperatures:
199+
raise ValueError(
200+
f"Expected {total_n_pressures * total_n_temperatures} unique lines, "
201+
f"but found {len(unique_lines)}."
202+
)
203+
# Write the merged output file
204+
merged_outfile = f"{outfile_base}.dat"
205+
with open(merged_outfile, "w") as outfile:
206+
outfile.writelines(header_lines)
207+
outfile.writelines(unique_lines)
208+
print(f"Merged output file created: {merged_outfile}")
94209

95-
# Create the BurnMan-readable table from the vertex output
96-
print("Creating BurnMan-readable table...")
97-
create_perplex_table(
98-
perplex_bindir,
99-
project_name,
100-
outfile,
101-
n_pressures,
102-
n_temperatures,
103-
pressure_range,
104-
temperature_range,
105-
)
106210
print("Processing complete.")

‎misc/ref/create_lo_res_table.py.out‎

Lines changed: 22 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,25 @@
11
Now working in newly created directory (iron_olivine_lo_res).
22
Creating local copies of requested thermodynamic data files...
3-
Making build file...
4-
Running vertex...
5-
Running pssect...
6-
Creating BurnMan-readable table...
3+
Creating table [1/2, 1/2]
4+
* Making build file...
5+
* Running vertex...
6+
* Running pssect...
7+
* Creating BurnMan-readable table...
8+
Creating table [1/2, 2/2]
9+
* Making build file...
10+
* Running vertex...
11+
* Running pssect...
12+
* Creating BurnMan-readable table...
13+
Creating table [2/2, 1/2]
14+
* Making build file...
15+
* Running vertex...
16+
* Running pssect...
17+
* Creating BurnMan-readable table...
18+
Creating table [2/2, 2/2]
19+
* Making build file...
20+
* Running vertex...
21+
* Running pssect...
22+
* Creating BurnMan-readable table...
23+
Merging output files...
24+
Merged output file created: iron_olivine_lo_res_table.dat
725
Processing complete.

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