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Fix NumPy version issue #343

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Merged
avcopan merged 1 commit into from
Mar 6, 2026
Merged

Fix NumPy version issue #343

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8 changes: 7 additions & 1 deletion src/mechanalyzer/calculator/bf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,12 @@
import numpy as np
import pandas as pd
from mechanalyzer import calculator
# AVC: Backward compatibility for numpy < 2.0, where the function is called `trapz`
try:
from numpy import trapezoid
except ImportError:
from numpy import trapz as trapezoid


######################## wrapper functions #########################################################

Expand Down Expand Up @@ -160,7 +166,7 @@ def bf_tp_df_full(ped_df, hotbf_df):
kind='cubic', fill_value=(hoten_spc.values[0], hoten_spc.values[-1]))
hoten_vect = f_hoten(ene_vect)
# recompute in an appropriate range
bf_series[spc] = np.trapz(ped_vect*hoten_vect, x=ene_vect)
bf_series[spc] = trapezoid(ped_vect*hoten_vect, x=ene_vect)
# renormalize for all species and put in dataframe
if any(bf_series.values < 0):
print('Warning: found negative BFs at {:1.0f} K and {:1.1e} atm'
Expand Down
23 changes: 14 additions & 9 deletions src/mechanalyzer/calculator/ene_partition.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,11 @@
from phydat import phycon
from mechanalyzer import calculator
from mechanalyzer.calculator.spinfo_frommess import get_dof_info_fromspcdct
# AVC: Backward compatibility for numpy < 2.0, where the function is called `trapz`
try:
from numpy import trapezoid
except ImportError:
from numpy import trapz as trapezoid


#################### wrapper function that calls the class ################################
Expand Down Expand Up @@ -144,7 +149,7 @@ def ped_df_rescale(starthot_df, ped_df_fromhot, save=False, name=''):
kernelsize)/kernelsize, mode='same')
cycles -= 1
# renormalize and put in dataframe
prob_vect /= np.trapz(prob_vect, x=ene_vect)
prob_vect /= trapezoid(prob_vect, x=ene_vect)
ped_df.at[temp, pressure] = pd.Series(prob_vect, index=ene_vect)
if ped_df[pressure][temp].empty:
T_del.append(temp)
Expand Down Expand Up @@ -280,7 +285,7 @@ def equip_simple(self):
for pressure in self.ped_df.columns:
for temp in self.ped_df.sort_index().index:
idx_new = self.ped_df[pressure][temp].index * beta_prod
norm_factor = np.trapz(
norm_factor = trapezoid(
self.ped_df[pressure][temp].values, x=idx_new)
vals = self.ped_df[pressure][temp].values/norm_factor
ped_df_prod.at[temp, pressure] = pd.Series(vals, index=idx_new)
Expand Down Expand Up @@ -348,7 +353,7 @@ def init_dos(pressure, temp):
rho_rovib_prod2[idx_ene_int] *
rho_trasl[idx_ene_minus_ene_int]
)
rho_non1.append(np.trapz(rho_non1_integrand,
rho_non1.append(trapezoid(rho_non1_integrand,
x=self.ene1_vect[idx_ene_int]))

rho_non1 = np.array(rho_non1)
Expand Down Expand Up @@ -378,7 +383,7 @@ def dos(idx_ene1, idx_ene_new):
# rhonon1(ene-ene1) with ene1<ene (fixed ene)
rho_non1_array = self.rho_non1[idx_ene_minus_ene1_array]
num = rho1_ene1 * rho_non1
den = np.trapz(rho1_ene1_array*rho_non1_array,
den = trapezoid(rho1_ene1_array*rho_non1_array,
x=self.ene1_vect[idx_ene1_array])
# if for some reason you get den=0: append 0 as value
if den == 0:
Expand Down Expand Up @@ -408,13 +413,13 @@ def dostherm_rhovibtrasl(idx_ene_vect, temp):
rho1_ene1_array = self.rho_rovib_prod1[idx_ene1_array]
rho_non1_array = self.rho_non1[idx_ene_minus_ene1_array]

rhotot_E1 = np.trapz(rho1_ene1_array*rho_non1_array,
rhotot_E1 = trapezoid(rho1_ene1_array*rho_non1_array,
x=self.ene1_vect[idx_ene1_array])

ene = self.ene1_vect[idx_ene1]
f_Etot_num.append(rhotot_E1*np.exp(-ene/phycon.RC_KCAL/temp))

den = np.trapz(f_Etot_num, x=self.ene1_vect[idx_ene_vect])
den = trapezoid(f_Etot_num, x=self.ene1_vect[idx_ene_vect])
f_Etot = pd.Series(
f_Etot_num/den, index=self.ene1_vect[idx_ene_vect])

Expand All @@ -425,7 +430,7 @@ def dostherm_rhovib(temp):
# rovib only
rho1_ene1_array = self.rho_rovib_prod1 * \
np.exp(-self.ene1_vect/phycon.RC_KCAL/temp)
den = np.trapz(rho1_ene1_array, x=self.ene1_vect)
den = trapezoid(rho1_ene1_array, x=self.ene1_vect)
f_Etot = pd.Series(rho1_ene1_array/den, index=self.ene1_vect)

return f_Etot
Expand Down Expand Up @@ -489,11 +494,11 @@ def dostherm_rhovib(temp):
ped_series.values[idx_ene_vect >= idx_ene1]
)

prob_ene1 = np.trapz(
prob_ene1 = trapezoid(
prob_ene1ene_tot_pressure_ped, ene_new)
prob_ene1_vect.append(prob_ene1)

norm_factor_prob_ene1 = np.trapz(
norm_factor_prob_ene1 = trapezoid(
prob_ene1_vect, x=self.ene1_vect)
prob_ene1_norm = prob_ene1_vect/norm_factor_prob_ene1

Expand Down
33 changes: 19 additions & 14 deletions src/mechanalyzer/tests/test__prompt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,11 @@
from mechanalyzer.calculator import spinfo_frommess
from mechanalyzer.calculator import ene_partition
from mechanalyzer.calculator import bf
# AVC: Backward compatibility for numpy < 2.0, where the function is called `trapz`
try:
from numpy import trapezoid
except ImportError:
from numpy import trapz as trapezoid

PATH = os.path.dirname(os.path.realpath(__file__))
INP_PATH = os.path.join(PATH, 'data', 'prompt', 'C3H8_OH')
Expand Down Expand Up @@ -70,8 +75,8 @@ def test_equip_simple():

assert np.isclose((ped_600.iloc[100]), 0.1043, atol=1e-4, rtol=1e-4)
assert np.isclose((ped_1200.iloc[100]), 0.02105, atol=1e-4, rtol=1e-4)
assert np.isclose(np.trapz(ped_600.values, x=ped_600.index), 1)
assert np.isclose(np.trapz(ped_1200.values, x=ped_1200.index), 1)
assert np.isclose(trapezoid(ped_600.values, x=ped_600.index), 1)
assert np.isclose(trapezoid(ped_1200.values, x=ped_1200.index), 1)


def test_equip_phi():
Expand All @@ -89,8 +94,8 @@ def test_equip_phi():

assert np.isclose((ped_600.iloc[166]), 0.045, atol=1e-3, rtol=1e-2)
assert np.isclose((ped_1200.iloc[166]), 0.0376, atol=1e-3, rtol=1e-2)
assert np.isclose(np.trapz(ped_600.values, x=ped_600.index), 1)
assert np.isclose(np.trapz(ped_1200.values, x=ped_1200.index), 1)
assert np.isclose(trapezoid(ped_600.values, x=ped_600.index), 1)
assert np.isclose(trapezoid(ped_1200.values, x=ped_1200.index), 1)


def test_beta_phi1a():
Expand All @@ -108,8 +113,8 @@ def test_beta_phi1a():

assert np.isclose((ped_400.iloc[166]), 0.001, atol=1e-3, rtol=1e-2)
assert np.isclose((ped_800.iloc[166]), 0.0589, atol=1e-3, rtol=1e-2)
assert np.isclose(np.trapz(ped_400.values, x=ped_400.index), 1)
assert np.isclose(np.trapz(ped_800.values, x=ped_800.index), 1)
assert np.isclose(trapezoid(ped_400.values, x=ped_400.index), 1)
assert np.isclose(trapezoid(ped_800.values, x=ped_800.index), 1)


def test_beta_phi2a():
Expand All @@ -127,8 +132,8 @@ def test_beta_phi2a():

assert np.isclose((ped_400.iloc[166]), 0.00045, atol=1e-4, rtol=1e-2)
assert np.isclose((ped_800.iloc[166]), 0.0522, atol=1e-3, rtol=1e-2)
assert np.isclose(np.trapz(ped_400.values, x=ped_400.index), 1)
assert np.isclose(np.trapz(ped_800.values, x=ped_800.index), 1)
assert np.isclose(trapezoid(ped_400.values, x=ped_400.index), 1)
assert np.isclose(trapezoid(ped_800.values, x=ped_800.index), 1)


def test_beta_phi3a():
Expand All @@ -146,8 +151,8 @@ def test_beta_phi3a():

assert np.isclose((ped_400.iloc[166]), 0.001, atol=1e-3, rtol=1e-2)
assert np.isclose((ped_800.iloc[166]), 0.0589, atol=1e-3, rtol=1e-2)
assert np.isclose(np.trapz(ped_400.values, x=ped_400.index), 1)
assert np.isclose(np.trapz(ped_800.values, x=ped_800.index), 1)
assert np.isclose(trapezoid(ped_400.values, x=ped_400.index), 1)
assert np.isclose(trapezoid(ped_800.values, x=ped_800.index), 1)


def test_rovib_dos():
Expand All @@ -167,8 +172,8 @@ def test_rovib_dos():

assert np.isclose((ped_1800.iloc[166]), 0.01985, atol=1e-3, rtol=1e-2)
assert np.isclose((ped_2000.iloc[166]), 0.01724, atol=1e-3, rtol=1e-2)
assert np.isclose(np.trapz(ped_1800.values, x=ped_1800.index), 1)
assert np.isclose(np.trapz(ped_2000.values, x=ped_2000.index), 1)
assert np.isclose(trapezoid(ped_1800.values, x=ped_1800.index), 1)
assert np.isclose(trapezoid(ped_2000.values, x=ped_2000.index), 1)


def test_thermal():
Expand All @@ -187,8 +192,8 @@ def test_thermal():

assert np.isclose((ped_1800.iloc[166]), 0.01924792, atol=1e-5, rtol=1e-5)
assert np.isclose((ped_2000.iloc[166]), 0.01132143, atol=1e-5, rtol=1e-5)
assert np.isclose(np.trapz(ped_1800.values, x=ped_1800.index), 1)
assert np.isclose(np.trapz(ped_2000.values, x=ped_2000.index), 1)
assert np.isclose(trapezoid(ped_1800.values, x=ped_1800.index), 1)
assert np.isclose(trapezoid(ped_2000.values, x=ped_2000.index), 1)


def test_bf_from_phi1a():
Expand Down
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