ararpy 0.1.30__py3-none-any.whl → 0.1.31__py3-none-any.whl

ararpy/__init__.py

@@ -16,7 +16,7 @@ from . import calc, smp, files, thermo, test
 """ Information """
 
 name = 'ararpy'
-version = '0.1.26'
+version = '0.1.31'
 __version__ = version
 full_version = version
 last_update = '2024-05-22'

ararpy/smp/corr.py

@@ -365,12 +365,12 @@ def calc_nor_inv_isochrons(sample: Sample):
     n = len(sample.SequenceName)
     try:
         isochron_1 = calc.isochron.get_data(
-            *calc.arr.mul(sample.DegasValues[20:22], sample.NormalizeFactor),
+            *calc.arr.mul(sample.DegasValues[20:22], sample.TotalParam[136:138]),
             *calc.arr.sub(sample.CorrectedValues[8:10], sample.DegasValues[30:32]),
             *sample.DegasValues[0:2]
         )
         isochron_2 = calc.isochron.get_data(
-            *calc.arr.mul(sample.DegasValues[20:22], sample.NormalizeFactor),
+            *calc.arr.mul(sample.DegasValues[20:22], sample.TotalParam[136:138]),
             *sample.DegasValues[0:2],
             *calc.arr.sub(sample.CorrectedValues[8:10], sample.DegasValues[30:32]))
     except (BaseException, Exception):
@@ -383,17 +383,17 @@ def calc_cl_isochrons(sample: Sample):
     n = len(sample.SequenceName)
     try:
         isochron_3 = calc.isochron.get_data(
-            *calc.arr.mul(sample.DegasValues[20:22], sample.NormalizeFactor),
+            *calc.arr.mul(sample.DegasValues[20:22], sample.TotalParam[136:138]),
             *sample.DegasValues[24:26],
-            *calc.arr.mul(sample.DegasValues[10:12], sample.NormalizeFactor))
+            *calc.arr.mul(sample.DegasValues[10:12], sample.TotalParam[136:138]))
         isochron_4 = calc.isochron.get_data(
-            *calc.arr.mul(sample.DegasValues[20:22], sample.NormalizeFactor),
-            *calc.arr.mul(sample.DegasValues[10:12], sample.NormalizeFactor),
+            *calc.arr.mul(sample.DegasValues[20:22], sample.TotalParam[136:138]),
+            *calc.arr.mul(sample.DegasValues[10:12], sample.TotalParam[136:138]),
             *sample.DegasValues[24:26])
         isochron_5 = calc.isochron.get_data(
-            *calc.arr.mul(sample.DegasValues[10:12], sample.NormalizeFactor),
+            *calc.arr.mul(sample.DegasValues[10:12], sample.TotalParam[136:138]),
             *sample.DegasValues[24:26],
-            *calc.arr.mul(sample.DegasValues[20:22], sample.NormalizeFactor))
+            *calc.arr.mul(sample.DegasValues[20:22], sample.TotalParam[136:138]))
     except (BaseException, Exception):
         return np.zeros([5, n]), np.zeros([5, n]), np.zeros([5, n])
     else:
@@ -451,7 +451,7 @@ def calc_ratio(sample: Sample, monte_carlo: bool = False):
         sample.ApparentAgeValues[0:2] = ar40aar36a
         sample.ApparentAgeValues[7] = ar36a_percent
     else:
-        ar39k, sar39k = calc.arr.mul(sample.DegasValues[20:22], sample.NormalizeFactor)
+        ar39k, sar39k = calc.arr.mul(sample.DegasValues[20:22], sample.TotalParam[136:138])
         sum_ar39k = sum(ar39k)
         ar39k_percent = [item / sum_ar39k * 100 if sum_ar39k != 0 else 0 for item in ar39k]
         ar40rar39k = calc.arr.mul_factor(
@@ -545,7 +545,7 @@ def monte_carlo_f(sample: Sample):
     R36v38clp = np.transpose(sample.TotalParam[56:58])
 
     stand_time_year = np.transpose(sample.TotalParam[32])
-    JNFactor = np.transpose(sample.NormalizeFactor)
+    JNFactor = np.transpose(sample.TotalParam[136:138])
 
     irradiation_cycles = [list(filter(None, re.split(r'[DS]', each_step))) for each_step in sample.TotalParam[27]]
     t1 = [re.findall(r"\d+", i) for i in sample.TotalParam[31]]  # t1: experimental times

ararpy/smp/initial.py

@@ -334,7 +334,7 @@ def check_version(smp: Sample):
             v, sv = smp.TotalParam[59:61]
     except:
         doNormalize = False
-    smp.NormalizeFactor = [
+    smp.TotalParam[136:138] = [
         [1 if v[0] == each or not doNormalize else v[0] / each for each in v],
         [0 if v[0] == v[i] or not doNormalize else err.div((v[0], sv[0]), (v[i], sv[i])) for i in range(len(v))]
     ]

ararpy/smp/plots.py

@@ -416,7 +416,7 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
     -------
     None
     """
-    ar39k, sar39k = calc.arr.mul(sample.DegasValues[20:22], sample.NormalizeFactor)
+    ar39k, sar39k = calc.arr.mul(sample.DegasValues[20:22], sample.TotalParam[136:138])
     ar40r, sar40r = sample.DegasValues[24:26]
     ar40rar39k = calc.arr.div([ar40r, sar40r], [ar39k, sar39k])
     params_initial_ratio = calc.arr.partial(sample.TotalParam, cols=list(range(115, 120)))
@@ -575,7 +575,7 @@ def recalc_mdf_plateaus(sample: Sample, **kwargs):
     -------
     None
     """
-    ar36a, sar36a = calc.arr.mul(sample.DegasValues[0:2], sample.NormalizeFactor)
+    ar36a, sar36a = calc.arr.mul(sample.DegasValues[0:2], sample.TotalParam[136:138])
     ar40aar36a = sample.ApparentAgeValues[0:2]
     mdf = sample.ApparentAgeValues[2:4]
 
@@ -613,7 +613,7 @@ def calc_ar40ar39(r, sr, smp):
     """
     try:
         ar36a = np.array(smp.DegasValues[0:2])
-        ar39k = calc.arr.mul(smp.DegasValues[20:22], smp.NormalizeFactor)
+        ar39k = calc.arr.mul(smp.DegasValues[20:22], smp.TotalParam[136:138])
         ar40 = smp.CorrectedValues[8:10]
         ar40k = smp.DegasValues[30:32]
         size = ar36a.shape[-1]

ararpy/smp/sample.py

@@ -169,6 +169,7 @@ TOTAL_PARAMS_HEADERS = [
     '38Ar Gain', '%1\u03C3',  # 132-133
     '39Ar Gain', '%1\u03C3',  # 134-135
     '40Ar Gain', '%1\u03C3',  # 136-137
+    'Normalize Factor', '1\u03C3',  # 138-139
 ]
 
 SAMPLE_INTERCEPT_SHORT_HEADERS = [
@@ -283,6 +284,7 @@ TOTAL_PARAMS_SHORT_HEADERS = [
     '38Gain', '%1s',  # 132-133
     '39Gain', '%1s',  # 134-135
     '40Gain', '%1s',  # 136-137
+    'NormalizeFactor', '1\u03C3',  # 138-139
 ]
 
 DEFAULT_PLOT_STYLES = lambda sample_type, age_unit: {
@@ -776,7 +778,7 @@ DEFAULT_PLOT_STYLES = lambda sample_type, age_unit: {
     },
 }
 
-VERSION = '20250622'
+VERSION = '20250806'
 
 NAMED_DICT = {
     "unknown": {"header": SAMPLE_INTERCEPT_HEADERS.copy()},
@@ -845,7 +847,6 @@ class Sample:
         self.SelectedSequence2 = []
         self.UnselectedSequence = []
         self.IsochronMark = []
-        self.NormalizeFactor = [[], []]
 
         # Tables and Plots
         self.UnknownTable = Table()

ararpy/thermo/atomic_level_random_walk.py

@@ -373,7 +373,7 @@ class DiffSimulation:
                         boundary_factor = 0.1 ** (k * math.log10(1 + (max(conditions[:, -1]) // 1000)))
                     step_length = self.step_length / np.sqrt(pos.shape[1] if len(pos.shape) > 1 else 1)
                     scale = int(total_steps)
-                    # print(f"调整后: {nsteps_factor = }, gamma = {conditions[0][-1]}, {total_steps = }, {compensation = }, {boundary_factor = }")
+                    print(f"调整后: {nsteps_factor = }, gamma = {conditions[0][-1]}, {total_steps = }, {compensation = }, {boundary_factor = }")
 
                     _pos = walker(
                         copy.deepcopy(pos), step_length=step_length, total_nsteps=total_steps,
@@ -437,7 +437,7 @@ class DiffSimulation:
                 self.remained_per_step.append(len(pos))
                 self.released_per_step.append(self.natoms - len(pos))
 
-            print(f"{index = } {duration} - {heating_duration = } - {temperature = } - {total_steps = } - conc = {len(pos) / self.natoms * 100:.2f}% - {time.time() - _start:.5f}s")
+            print(f"{index = } {duration = }s - {heating_duration = }s - {temperature = }K - {total_steps = } - conc = {len(pos) / self.natoms * 100:.2f}% - {time.time() - _start:.5f}s")
 
         self.positions = copy.deepcopy(pos)
 
@@ -452,6 +452,49 @@ class DiffSimulation:
         return self.run_sequence(*seq, domains=domains, nsteps_factor=scale, simulating=simulation,
                                  epsilon=epsilon, start_time=start_time)
 
+def demo_init(n, es, fs, di, gs, ds, fr, ss=1):
+    demo = DiffSimulation()
+    # fs 应从大到小，父空间在前，子空间在后
+
+    # demo.grain_size = 300
+    # demo.size_scale = 0.05
+    # demo.atom_density = 1e14  # 原子密度 个/立方厘米
+
+    demo.dimension = di                 # dimension, 1 or 3
+    demo.size_scale = 1                 # size_scale
+    demo.grain_size = gs                # grain_szie
+    demo.frequency = fr                 # frequency
+
+    # domains应该从外到内
+    domains = []
+    for i in range(n-1, 0-1, -1):
+        size = int(demo.grain_size * fs[i]) * demo.size_scale
+        center = np.zeros(demo.dimension)
+        if isinstance(ds, (int, float)) or len(ds) == 1:
+            demo.atom_density = ds              # atom_density  # 原子密度 个/立方厘米
+            if i == 2:
+                ad = ds * 5 / 4
+            else:
+                ad = ds
+        else:
+            ad = ds[i]
+        dom = Domain(
+            dimension=demo.dimension, atom_density=ad, min_bound=center - size / 2, max_bound=center + size / 2,
+            energy=es[i], fraction=fs[i], inclusions=[domains[-1]] if len(domains) >= 1 else []
+        )
+        domains.append(dom)
+    # domains应该从外到内, 上面为了inclusion以及方便不同扩散域设置不同的密度，要按照从小到大的顺序生成，但是后面行走的时候要根据不同条件设置系数，要从外到内
+    demo.domains = sorted(domains, key=lambda dom: dom.fraction, reverse=True)
+
+    demo.setup()
+
+    a = [f"{dom.fraction = }, {dom.energy = }, {dom.natoms = }, {dom.atom_density = }" for dom in demo.domains]
+
+    print(
+        f"Total Atoms: {demo.natoms}\n" + "\n".join(a)
+    )
+
+    return demo
 
 def run(times, temps, statuses, energies, fractions, ndoms: int = 1, grain_szie=275, atom_density=1e10, frequency=1e13,
         dimension: int = 3, targets: list = None, epsilon: float = 0.001, simulation: bool = False,
@@ -472,57 +515,19 @@ def run(times, temps, statuses, energies, fractions, ndoms: int = 1, grain_szie=
     :return:
     """
 
-    demo = DiffSimulation()
-
-    def _(n, es, fs):
-        # fs 应从大到小，父空间在前，子空间在后
-
-        # demo.grain_size = 300
-        # demo.size_scale = 0.05
-        # demo.atom_density = 1e14  # 原子密度 个/立方厘米
-        demo.dimension = dimension
-
-        demo.size_scale = 1
-        demo.grain_size = grain_szie
-        demo.atom_density = atom_density  # 原子密度 个/立方厘米
-        demo.frequency = frequency
-
-        # domains应该从外到内
-        domains = []
-        for i in range(n-1, 0-1, -1):
-            size = int(demo.grain_size * fs[i]) * demo.size_scale
-            center = np.zeros(demo.dimension)
-            if i == 2:
-                ad = demo.atom_density * 5 / 4
-            else:
-                ad = demo.atom_density
-            dom = Domain(
-                dimension=demo.dimension, atom_density=ad, min_bound=center - size / 2, max_bound=center + size / 2,
-                energy=es[i], fraction=fs[i], inclusions=[domains[-1]] if len(domains) >= 1 else []
-            )
-            domains.append(dom)
-        # domains应该从外到内, 上面为了inclusion以及方便不同扩散域设置不同的密度，要按照从小到大的顺序生成，但是后面行走的时候要根据不同条件设置系数，要从外到内
-        demo.domains = sorted(domains, key=lambda dom: dom.fraction, reverse=True)
-
-        demo.setup()
-
+    try:
+        # demo.run_persecond(times=times, temperatures=temps, domains=demo.domains, targets=target,
+        #                    epsilon=epsilon, simulation=simulation)
+        demo = demo_init(ndoms, energies, fractions, dimension, grain_szie, atom_density, frequency, ss=1)
         demo.name = f"{file_name}"
 
-        print(f"Total Atoms: {demo.natoms}, atoms in each dom: {[dom.natoms for dom in demo.domains]} filename: {demo.name}")
-
         if positions is not None:
             demo.positions = positions
             demo.natoms = len(positions)
 
         demo.run_sequence(times=times, temperatures=temps, statuses=statuses, targets=targets, domains=demo.domains,
                           epsilon=epsilon, simulating=simulation, **kwargs)
-        # demo.run_persecond(times=times, temperatures=temps, domains=demo.domains, targets=target,
-        #                    epsilon=epsilon, simulation=simulation)
-
-        return demo
-
-    try:
-        return _(ndoms, energies, fractions), True
+        return demo, True
     except OverEpsilonError as e:
         if ignore_error:
             return demo, False

{ararpy-0.1.30.dist-info → ararpy-0.1.31.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.1.30
+Version: 0.1.31
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.1.30.dist-info → ararpy-0.1.31.dist-info}/RECORD

@@ -1,4 +1,4 @@
-ararpy/__init__.py,sha256=vsCWb5yzto-kGLLNpOzAb74KvfITyybMQ5RgEJJkmlU,6857
+ararpy/__init__.py,sha256=4NVQopyzptK_z2c7IrMwGSekzQ2reMbk0O2dSq9Maxw,6857
 ararpy/test.py,sha256=4F46-JJ1Ge12HGae0qO44Qc6kiEMHBgn2MsY_5LlHDo,3973
 ararpy/calc/__init__.py,sha256=kUjRuLE8TLuKOv3i976RnGJoEMj23QBZDu37LWs81U4,322
 ararpy/calc/age.py,sha256=WOZs70zXiBWDIEhXJLIaNiYTOFJNk0NDbH5e5zCbCks,5435
@@ -44,23 +44,23 @@ ararpy/smp/__init__.py,sha256=k6_fa27UJsQK7K7oC5GYlwMo6l0Xd8af3QtOrZz2XJk,478
 ararpy/smp/basic.py,sha256=PMvlSoToY8CJEORRrhEo4rYM2-VfSmjg0IuDpGFOGUM,24899
 ararpy/smp/calculation.py,sha256=LCFJWjLVLEKEQ5b7RFUIxsMahEzgLdodW4kCYXV5Z34,2919
 ararpy/smp/consts.py,sha256=XIdjdz8cYxspG2jMnoItdlUsxr3hKbNFJjMZJh1bpzw,393
-ararpy/smp/corr.py,sha256=TzH7rymToJP0RCI0pQm-SrqnwAZ58HJbxahE8chv2wQ,26511
+ararpy/smp/corr.py,sha256=U5K1Vld55IHea_fZ7EEY_8dkvjp0f6OhpdSxf7b9WGY,26551
 ararpy/smp/diffusion_funcs.py,sha256=4-PMMIZWzjk2HOYYWNgSp4GmApygp1MmOxJ2g3xrqWc,175049
 ararpy/smp/export.py,sha256=eBUGx9eUHQ7EoibT-PC1HK7Zw_V1LUfuKJv56_XccUQ,117284
 ararpy/smp/info.py,sha256=iKUELm-BuUduDlJKC1d8tKKNHbwwbNmhUg2pi6bcBvA,489
-ararpy/smp/initial.py,sha256=GFLEYxes-_PT_qgZj0Dagy_blg9JmzjO7uh3vQHbS78,17891
+ararpy/smp/initial.py,sha256=YjHpdzlMxRQXyBOMe9Kd3-nNsjPjCWCub5mUcnprhAw,17895
 ararpy/smp/json.py,sha256=BTZCjVN0aj9epc700nwkYEYMKN2lHBYo-pLmtnz5oHY,2300
-ararpy/smp/plots.py,sha256=rF0vrFu9dMt2Eu1EHiDfDRC9232M6dH0Unc_3qNDxLY,33579
+ararpy/smp/plots.py,sha256=9w20cne704jmJl4btWk0LWcrHRqV5-DQmgG3Cq_GeEk,33591
 ararpy/smp/raw.py,sha256=51n-rrbW2FqeZHQyevuG7iObPLGvIBzTe414QDVM1FE,6523
-ararpy/smp/sample.py,sha256=slKiGUobEG7ZfJW6byBgc9jlWN1-zLg27iEdm-No5dw,58228
+ararpy/smp/sample.py,sha256=JVHCYOxZm_So1UXWcWIsMWz0pbPayR0gSrolxOGuUu4,58280
 ararpy/smp/style.py,sha256=wCygwtpCflhzwmI7u08X-feYGPytOyfR98YcgJx813c,7678
 ararpy/smp/table.py,sha256=9bNAOqAIOc0nSC3LNeqjJKUYSJSM28Ji3o9VimwMU8A,6645
 ararpy/thermo/__init__.py,sha256=6VBuqTRFl403PVqOuMkVrut0nKaQsAosBmfW91X1dMg,263
 ararpy/thermo/arrhenius.py,sha256=Ass1ichHfqIAtpv8eLlgrUc1UOb3Urh1qzr1E3gLB4U,233
-ararpy/thermo/atomic_level_random_walk.py,sha256=Q97zfe2h2RaxADkoBAqd0uEiP16BFOajrTmXHMkL2EQ,25502
+ararpy/thermo/atomic_level_random_walk.py,sha256=kmP1Fu3wZhIJqxvOJIWbO8rFsSBMKE-6lrBA8oJtuP8,25772
 ararpy/thermo/basic.py,sha256=nBGHI9uK7VdJwThwBIOcKAzdnYqPyQseFoY6s4zKizk,11504
-ararpy-0.1.30.dist-info/licenses/LICENSE,sha256=cvG5t_C1qY_zUyJI7sNOa7gCArdngNPaOrfujl2LYuc,1085
-ararpy-0.1.30.dist-info/METADATA,sha256=OkwCC5DEb-8Q_ZtpeNhcLuYsBvA6nzyVQ6ZMpRYjkko,24516
-ararpy-0.1.30.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-ararpy-0.1.30.dist-info/top_level.txt,sha256=9iTpsPCYuRYq09yQTk9d2lqB8JtTEOmbN-IcGB-K3vY,7
-ararpy-0.1.30.dist-info/RECORD,,
+ararpy-0.1.31.dist-info/licenses/LICENSE,sha256=cvG5t_C1qY_zUyJI7sNOa7gCArdngNPaOrfujl2LYuc,1085
+ararpy-0.1.31.dist-info/METADATA,sha256=zhXfAk7Vx34WjBVUE_jSw4rM27BuSom462BCxssWvvU,24516
+ararpy-0.1.31.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+ararpy-0.1.31.dist-info/top_level.txt,sha256=9iTpsPCYuRYq09yQTk9d2lqB8JtTEOmbN-IcGB-K3vY,7
+ararpy-0.1.31.dist-info/RECORD,,