ararpy 0.1.30__py3-none-any.whl → 0.1.33__py3-none-any.whl

ararpy/smp/sample.py

@@ -22,25 +22,25 @@ from types import MethodType
 import pandas as pd
 
 SAMPLE_INTERCEPT_HEADERS = [
-    'Sequence', '',  # 0-1
+    'Sequence', '', 'Mark',  # 0-2
     '\u00B3\u2076Ar', '1\u03C3', '\u00B3\u2077Ar', '1\u03C3',  # 2-5
     '\u00B3\u2078Ar', '1\u03C3', '\u00B3\u2079Ar', '1\u03C3',  # 6-9
     '\u2074\u2070Ar', '1\u03C3',  # 10-11
 ]
 BLANK_INTERCEPT_HEADERS = [
-    'Sequence', '',  # 0-1
+    'Sequence', '', 'Mark',  # 0-2
     '\u00B3\u2076Ar', '1\u03C3', '\u00B3\u2077Ar', '1\u03C3',  # 2-5
     '\u00B3\u2078Ar', '1\u03C3', '\u00B3\u2079Ar', '1\u03C3',  # 6-9
     '\u2074\u2070Ar', '1\u03C3',  # 10-11
 ]
 CORRECTED_HEADERS = [
-    'Sequence', '',  # 0-1
+    'Sequence', '', 'Mark',  # 0-2
     '\u00B3\u2076Ar', '1\u03C3', '\u00B3\u2077Ar', '1\u03C3',  # 2-5
     '\u00B3\u2078Ar', '1\u03C3', '\u00B3\u2079Ar', '1\u03C3',  # 6-9
     '\u2074\u2070Ar', '1\u03C3',  # 10-11
 ]
 DEGAS_HEADERS = [
-    'Sequence', '',  # 0-1
+    'Sequence', '', 'Mark',  # 0-2
     '\u00B3\u2076Ar[a]', '1\u03C3', '\u00B3\u2076Ar[c]', '1\u03C3',  # 2-5
     '\u00B3\u2076Ar[Ca]', '1\u03C3', '\u00B3\u2076Ar[Cl]', '1\u03C3',  # 6-9
     '\u00B3\u2077Ar[Ca]', '1\u03C3', '\u00B3\u2078Ar[Cl]', '1\u03C3',  # 10-13
@@ -51,40 +51,40 @@ DEGAS_HEADERS = [
     '\u2074\u2070Ar[c]', '1\u03C3', '\u2074\u2070Ar[K]', '1\u03C3'  # 30-33
 ]
 PUBLISH_TABLE_HEADERS = [
-    'Sequence', '',  # 0-1
+    'Sequence', '', 'Mark',  # 0-2
     '\u00B3\u2076Ar[a]', '\u00B3\u2077Ar[Ca]', '\u00B3\u2078Ar[Cl]',  # 2-4
     '\u00B3\u2079Ar[K]', '\u2074\u2070Ar[r]',  # 5-6
     'Apparent Age', '1\u03C3', '\u2074\u2070Ar[r]%', '\u00B3\u2079Ar[K]%',  # 7-10
     'Ca/K', '1\u03C3',  # 11-12
 ]
 PUBLISH_TABLE_HEADERS_AIR = [
-    'Sequence', '',  # 0-1
+    'Sequence', '', 'Mark',  # 0-2
     '\u00B3\u2076Ar[a]', '\u00B3\u2077Ar[Ca]', '\u00B3\u2078Ar[Cl]',  # 2-4
     '\u00B3\u2079Ar[K]', '\u2074\u2070Ar[r]',  # 5-6
     'MDF', '1\u03C3', '\u2074\u2070Ar[r]%', '\u00B3\u2076Ar%',  # 7-10
     'Ca/K', '1\u03C3',  # 11-12
 ]
 PUBLISH_TABLE_HEADERS_STD = [
-    'Sequence', '',  # 0-1
+    'Sequence', '', 'Mark',  # 0-2
     '\u00B3\u2076Ar[a]', '\u00B3\u2077Ar[Ca]', '\u00B3\u2078Ar[Cl]',  # 2-4
     '\u00B3\u2079Ar[K]', '\u2074\u2070Ar[r]',  # 5-6
     'J', '1\u03C3', '\u2074\u2070Ar[r]%', '\u00B3\u2076Ar%',  # 7-10
     'Ca/K', '1\u03C3',  # 11-12
 ]
 SPECTRUM_TABLE_HEADERS = [
-    'Sequence', '',  # 0-1
+    'Sequence', '', 'Mark',  # 0-2
     '\u2074\u2070Ar/\u00B3\u2079Ar', '1\u03C3',  # 2-3
     'Apparent Age', '1\u03C3', '1\u03C3', '1\u03C3',  # 4-7
     '\u2074\u2070Ar[r]%', '\u00B3\u2079Ar[K]%',  # 8-9
 ]
 SPECTRUM_TABLE_HEADERS_AIR = [
-    'Sequence', '',  # 0-1
+    'Sequence', '', 'Mark',  # 0-2
     '\u2074\u2070Ar/\u00B3\u2076Ar', '1\u03C3',  # 2-3
     'MDF', '1\u03C3', '1\u03C3', '1\u03C3',  # 4-7
     '\u2074\u2070Ar[r]%', '\u00B3\u2076Ar%',  # 8-9
 ]
 SPECTRUM_TABLE_HEADERS_STD = [
-    'Sequence', '',  # 0-1
+    'Sequence', '', 'Mark',  # 0-2
     '\u2074\u2070Ar/\u00B3\u2076Ar', '1\u03C3',  # 2-3
     'J', '1\u03C3', '1\u03C3', '1\u03C3',  # 4-7
     '\u2074\u2070Ar[r]%', '\u00B3\u2076Ar%',  # 8-9
@@ -107,7 +107,7 @@ ISOCHRON_TABLE_HEADERS = [
     'r1', 'r2', 'r3',  # 39-41
 ]
 TOTAL_PARAMS_HEADERS = [
-    'Sequence', '',  # 0-1
+    'Sequence', '', 'Mark',  # 0-2
     '(\u2074\u2070Ar/\u00B3\u2076Ar)t', '%1\u03C3',
     '(\u2074\u2070Ar/\u00B3\u2076Ar)c', '%1\u03C3',  # 2-5
     '(\u00B3\u2078Ar/\u00B3\u2076Ar)t', '%1\u03C3',
@@ -169,22 +169,26 @@ 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 = [
-    'Seq', 'Label', 'Ar36', '1s', 'Ar37', '1s',
+    'Seq', 'Label', 'Mark',  # 0-2
+    'Ar36', '1s', 'Ar37', '1s',
     'Ar38', '1s', 'Ar39', '1s', 'Ar40', '1s'
 ]
 BLANK_INTERCEPT_SHORT_HEADERS = [
-    'Seq', 'Label', 'Ar36', '1s', 'Ar37', '1s',
+    'Seq', 'Label', 'Mark',  # 0-2
+    'Ar36', '1s', 'Ar37', '1s',
     'Ar38', '1s', 'Ar39', '1s', 'Ar40', '1s'
 ]
 CORRECTED_SHORT_HEADERS = [
-    'Seq', 'Label', 'Ar36', '1s', 'Ar37', '1s',
+    'Seq', 'Label', 'Mark',  # 0-2
+    'Ar36', '1s', 'Ar37', '1s',
     'Ar38', '1s', 'Ar39', '1s', 'Ar40', '1s'
 ]
 DEGAS_SHORT_HEADERS = [
-    'Seq', 'Label',  # 0-1
+    'Seq', 'Label', 'Mark',  # 0-2
     'Ar36[a]', '1s', 'Ar36[c]', '1s',  # 2-5
     'Ar36[Ca]', '1s', 'Ar36[Cl]', '1s',  # 6-9
     'Ar37[Ca]', '1s', 'Ar38[Cl]', '1s',  # 10-13
@@ -195,12 +199,14 @@ DEGAS_SHORT_HEADERS = [
     'Ar40[c]', '1s', 'Ar40[K]', '1s'  # 29-32
 ]
 PUBLISH_TABLE_SHORT_HEADERS = [
-    'Seq', 'Label', 'Ar36[a]', 'Ar37[Ca]', 'Ar38[Cl]',
+    'Seq', 'Label', 'Mark',  # 0-2
+    'Ar36[a]', 'Ar37[Ca]', 'Ar38[Cl]',
     'Ar39[K]', 'Ar40[r]', 'Apparent Age', '1s', 'Ar40r%',
     'Ar39K%', 'Ca/K', '1s'
 ]
 SPECTRUM_TABLE_SHORT_HEADERS = [
-    'Seq', 'Label', 'Ar40/Ar39', '1s', 'Apparent Age',
+    'Seq', 'Label', 'Mark',  # 0-2
+    'Ar40/Ar39', '1s', 'Apparent Age',
     '1s', '1s', '1s', 'Ar40[r]%', 'Ar39[K]%'
 ]
 ISOCHRON_TABLE_SHORT_HEADERS = [
@@ -221,7 +227,7 @@ ISOCHRON_TABLE_SHORT_HEADERS = [
     'r1', 'r2', 'r3',  # 39-41
 ]
 TOTAL_PARAMS_SHORT_HEADERS = [
-    'Seq', 'Label',  # 0-1
+    'Seq', 'Label', 'Mark',  # 0-2
     'T_40v36', '%1s',
     'C_40v36', '%1s',  # 2-5
     'T_38v36', '%1s',
@@ -283,6 +289,7 @@ 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 +783,7 @@ DEFAULT_PLOT_STYLES = lambda sample_type, age_unit: {
     },
 }
 
-VERSION = '20250622'
+VERSION = '20251001'
 
 NAMED_DICT = {
     "unknown": {"header": SAMPLE_INTERCEPT_HEADERS.copy()},
@@ -845,7 +852,6 @@ class Sample:
         self.SelectedSequence2 = []
         self.UnselectedSequence = []
         self.IsochronMark = []
-        self.NormalizeFactor = [[], []]
 
         # Tables and Plots
         self.UnknownTable = Table()
@@ -885,7 +891,8 @@ class Sample:
         # self.__version = '20250321'  # error sigma adjustment
         # self.__version = '20250328'  # Experiment info
         # self.__version = '20250404'  # J normalization factor
-        self.__version = '20250622'  # version setter
+        # self.__version = '20251001'  # add marker col for all tables
+        self.__version = '20251001'  # version setter
 
     @property
     def version(self):
@@ -1014,17 +1021,25 @@ class Table:
             setattr(self, k, v)
         self.set_coltypes()
 
-    def set_coltypes(self):
-        for i in self.text_indexes:
-            if i < self.colcount:
+    def set_coltypes(self, text_indexes=None):
+        if text_indexes is not None:
+            self.text_indexes = text_indexes
+        if not isinstance(self.text_indexes, list):
+            raise TypeError(f"Text_indexes is not allowed: {self.text_indexes}")
+        for i in range(self.colcount):
+            if i in self.text_indexes:
                 self.coltypes[i].update({'type': 'text'})
-        for i in self.numeric_indexes:
-            if i < self.colcount:
+            else:
                 self.coltypes[i].update({
                     'type': 'numeric',
                     'numericFormat': {'pattern': {'mantissa': self.decimal_places}},
                 })
 
+    def set_colcount(self, c: int):
+        self.colcount = c
+        while len(self.coltypes) < c:
+            self.coltypes.append({'type': 'text'})
+
 
 class Plot:
     def __init__(self, id='', type='', name='', data=None, info=None, **kwargs):

ararpy/smp/style.py

@@ -195,9 +195,11 @@ def set_table_style(sample: Sample):
     -------
 
     """
+    std = initial.initial(Sample())
     for key, comp in basic.get_components(sample).items():
         if isinstance(comp, Table):
             comp.header = TABLEHEADER(sample_type=sample.Info.sample.type, index=int(comp.id))
+            comp.text_indexes = basic.get_component_byid(std, comp.id).text_indexes
             comp.set_coltypes()
             # comp.colcount = len(comp.header)
             # comp.coltypes = [{'type': 'numeric'}] * (comp.colcount)

ararpy/smp/table.py

@@ -39,16 +39,16 @@ def update_table_data(smp: Sample, only_table: str = None):
             continue
         if key == '1':
             data = calc.arr.merge(
-                smp.SequenceName, smp.SequenceValue, *smp.SampleIntercept)
+                smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.SampleIntercept)
         elif key == '2':
             data = calc.arr.merge(
-                smp.SequenceName, smp.SequenceValue, *smp.BlankIntercept)
+                smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.BlankIntercept)
         elif key == '3':
             data = calc.arr.merge(
-                smp.SequenceName, smp.SequenceValue, *smp.CorrectedValues)
+                smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.CorrectedValues)
         elif key == '4':
             data = calc.arr.merge(
-                smp.SequenceName, smp.SequenceValue, *smp.DegasValues)
+                smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.DegasValues)
         elif key == '5':
             smp.PublishValues[0] = copy.deepcopy(smp.DegasValues[ 0])
             smp.PublishValues[1] = copy.deepcopy(smp.DegasValues[ 8])
@@ -58,19 +58,20 @@ def update_table_data(smp: Sample, only_table: str = None):
             smp.PublishValues[5:7] = copy.deepcopy(smp.ApparentAgeValues[2:4])
             smp.PublishValues[7:9] = copy.deepcopy(smp.ApparentAgeValues[6:8])
             data = calc.arr.merge(
-                smp.SequenceName, smp.SequenceValue, *smp.PublishValues)
+                smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.PublishValues)
         elif key == '6':
             data = calc.arr.merge(
-                smp.SequenceName, smp.SequenceValue, *smp.ApparentAgeValues)
+                smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.ApparentAgeValues)
         elif key == '7':
             data = calc.arr.merge(
                 smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.IsochronValues)
         elif key == '8':
             data = calc.arr.merge(
-                smp.SequenceName, smp.SequenceValue, *smp.TotalParam)
+                smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.TotalParam)
         else:
             data = [['']]
         # calc.arr.replace(data, pd.isnull, None)
+        comp.set_colcount(len(data))
         setattr(comp, 'data', calc.arr.transpose(data))
 
 
@@ -111,42 +112,43 @@ def update_handsontable(smp: Sample, data: list, id: str):
 
     update_all_table = False
     try:
-        if data[1] != smp.SequenceValue:
+        if data[1] != smp.SequenceValue or data[2] != smp.IsochronMark:
             update_all_table = True
             smp.SequenceValue = data[1]
+            smp.IsochronMark = data[2]
     except IndexError:
+        print(f"Check sequence value / isochron mark failed")
         pass
 
     if id == '1':  # 样品值
-        data = _normalize_data(data, len(samples.SAMPLE_INTERCEPT_HEADERS), 2)
+        data = _normalize_data(data, len(samples.SAMPLE_INTERCEPT_HEADERS), 3)
         smp.SampleIntercept = _digitize_data(data)
     elif id == '2':  # 本底值
-        data = _normalize_data(data, len(samples.BLANK_INTERCEPT_HEADERS), 2)
+        data = _normalize_data(data, len(samples.BLANK_INTERCEPT_HEADERS), 3)
         smp.BlankIntercept = _digitize_data(data)
     elif id == '3':  # 校正值
-        data = _normalize_data(data, len(samples.CORRECTED_HEADERS), 2)
+        data = _normalize_data(data, len(samples.CORRECTED_HEADERS), 3)
         smp.CorrectedValues = _digitize_data(data)
     elif id == '4':  # Degas table
-        data = _normalize_data(data, len(samples.DEGAS_HEADERS), 2)
+        data = _normalize_data(data, len(samples.DEGAS_HEADERS), 3)
         smp.DegasValues = _digitize_data(data)
     elif id == '5':  # 发行表
-        data = _normalize_data(data, len(samples.PUBLISH_TABLE_HEADERS), 2)
+        data = _normalize_data(data, len(samples.PUBLISH_TABLE_HEADERS), 3)
         smp.PublishValues = _digitize_data(data)
     elif id == '6':  # 年龄谱
-        data = _normalize_data(data, len(samples.SPECTRUM_TABLE_HEADERS), 2)
+        data = _normalize_data(data, len(samples.SPECTRUM_TABLE_HEADERS), 3)
         smp.ApparentAgeValues = _digitize_data(data)
     elif id == '7':  # 等时线
-        smp.IsochronMark = _digitize_data(data)[2]
         data = _normalize_data(data, len(samples.ISOCHRON_TABLE_HEADERS), 3)
         smp.IsochronValues = _digitize_data(data)
-        smp.sequence()
     elif id == '8':  # 总参数
-        data = _normalize_data(data, len(samples.TOTAL_PARAMS_HEADERS), 2)
+        data = _normalize_data(data, len(samples.TOTAL_PARAMS_HEADERS), 3)
         data = _digitize_data(data)
         data[101: 112] = [_strToBool(i) for i in data[101: 112]]
         smp.TotalParam = data
     else:
         raise ValueError(f"{id = }, The table id is not supported.")
+    smp.sequence()
     if update_all_table:
         update_table_data(smp)
     else:
@@ -171,21 +173,21 @@ def update_data_from_table(smp: Sample, only_table: str = None):
         if only_table is not None and key != only_table:
             continue
         if key == '1':
-            smp.SampleIntercept = calc.arr.transpose(comp.data)[2:]
+            smp.SampleIntercept = calc.arr.transpose(comp.data)[3:]
         elif key == '2':
-            smp.BlankIntercept = calc.arr.transpose(comp.data)[2:]
+            smp.BlankIntercept = calc.arr.transpose(comp.data)[3:]
         elif key == '3':
-            smp.CorrectedValues = calc.arr.transpose(comp.data)[2:]
+            smp.CorrectedValues = calc.arr.transpose(comp.data)[3:]
         elif key == '4':
-            smp.DegasValues = calc.arr.transpose(comp.data)[2:]
+            smp.DegasValues = calc.arr.transpose(comp.data)[3:]
         elif key == '5':
-            smp.PublishValues = calc.arr.transpose(comp.data)[2:]
+            smp.PublishValues = calc.arr.transpose(comp.data)[3:]
         elif key == '6':
-            smp.ApparentAgeValues = calc.arr.transpose(comp.data)[2:]
+            smp.ApparentAgeValues = calc.arr.transpose(comp.data)[3:]
         elif key == '7':
             smp.IsochronValues = calc.arr.transpose(comp.data)[3:]
         elif key == '8':
-            smp.TotalParam = calc.arr.transpose(comp.data)[2:]
+            smp.TotalParam = calc.arr.transpose(comp.data)[3:]
         else:
             pass
 

ararpy/thermo/atomic_level_random_walk.py

@@ -127,8 +127,9 @@ def walker2(pos: np.ndarray, duration, step_length, min_bound, max_bound, time_s
     :return:
     """
 
-    if len(pos) == 0:
-        return pos
+    # Ar40模拟时不能判断，因为会增加
+    # if len(pos) == 0:
+    #     return pos
 
     dimension = pos.shape[-1] if len(pos.shape) > 1 else 1
 
@@ -141,7 +142,6 @@ def walker2(pos: np.ndarray, duration, step_length, min_bound, max_bound, time_s
             conditions = np.array([[-50, -50, 50, 50, 1]])
 
     for step in range(int(1e16)):
-
         n = parent - int(parent * math.exp(-1 * decay * dt / (3600 * 24 * 365.2425)))
         # print(f"number of new pos = {n}")
         parent = parent - n
@@ -288,6 +288,8 @@ class DiffSimulation:
         self.end_at = 0
         self.dimension = 3
 
+        self.thermal_log = []
+
         self.size_scale = 1
         self.length_scale = 1
 
@@ -373,7 +375,7 @@ 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 +439,7 @@ 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 +454,49 @@ 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,
@@ -472,43 +517,12 @@ 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}")
+        demo.thermal_log = list(zip(times, temps))
 
         if positions is not None:
             demo.positions = positions
@@ -516,13 +530,7 @@ def run(times, temps, statuses, energies, fractions, ndoms: int = 1, grain_szie=
 
         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/thermo/basic.py

@@ -235,7 +235,7 @@ def get_tc(da2, sda2, E, sE, cooling_rate=10, temp_in_celsius=True, temp=None, A
     R = 8.314 if R is None else R # in J/K mol
     Tc = 600
     sTc = 0
-    Tm = 99999999 if temp is None else temp
+    Tm = 9999999999 if temp is None else temp
     Tm = Tm + 273.15 if temp_in_celsius else Tm
     cooling_rate = cooling_rate / 1000000
 
@@ -243,8 +243,8 @@ def get_tc(da2, sda2, E, sE, cooling_rate=10, temp_in_celsius=True, temp=None, A
     iter_diff = 100
     while abs(iter_diff) > 0.01 and iter_num < 100:
         tau = R * Tc ** 2 / (E * cooling_rate)
-        # new_Tc = (E/R) / log(A * tau * da2)
         new_Tc = (R / E) * log(A * tau * da2) + 1 / Tm  #
+        # new_Tc = (R / E) * log(A * tau * da2)
         d1 = cooling_rate / (A * da2 * Tc ** 2)
         s1 = d1 ** 2 * sda2 ** 2  # da2
         d2 = R / E ** 2 * (log(A * tau * da2) + 1)

{ararpy-0.1.30.dist-info → ararpy-0.1.33.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.1.30
+Version: 0.1.33
 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-0.1.33.dist-info}/RECORD

@@ -1,4 +1,11 @@
-ararpy/__init__.py,sha256=vsCWb5yzto-kGLLNpOzAb74KvfITyybMQ5RgEJJkmlU,6857
+ararpy/Example - Check arr.py,sha256=c9HUUZySUXOYk4eCqiPSp124G2sYpFP5zoMl0FXdalE,1709
+ararpy/Example - Granite Cooling History.py,sha256=V4V63RVp1gocOZX0T3OOGOiVhCA1DqrCyJnXgFvEcUs,14917
+ararpy/Example - Plot temperature calibration.py,sha256=8pR-WKqdaIKQTuuSbfwXuxoEkCop4zhmZUMJSARWDOg,10879
+ararpy/Example - Show MDD results.py,sha256=YFkiQual60lyCClsfvivr4REY6waSYuomf0uo5soUHE,22635
+ararpy/Example - Show all Kfs age spectra.py,sha256=1edPtBpFfS0lC7vLnLu34mDHt_xjbc8ptk6rZ--pf-I,12304
+ararpy/Example - Show random walk results.py,sha256=8WWvbAI7ySiMR-XwtFe5kTQihW3mcqzL3S7EUZdoxYo,15477
+ararpy/Example - Tc calculation.py,sha256=sD9pu3IaZ8mBV95rV2wOEhlQUexFNqBUoBqnNMdUBis,19617
+ararpy/__init__.py,sha256=gPUEjLwZfmGeG3RpVZntFrR9QpnFevpxiyACtYq_gtk,6857
 ararpy/test.py,sha256=4F46-JJ1Ge12HGae0qO44Qc6kiEMHBgn2MsY_5LlHDo,3973
 ararpy/calc/__init__.py,sha256=kUjRuLE8TLuKOv3i976RnGJoEMj23QBZDu37LWs81U4,322
 ararpy/calc/age.py,sha256=WOZs70zXiBWDIEhXJLIaNiYTOFJNk0NDbH5e5zCbCks,5435
@@ -10,8 +17,8 @@ ararpy/calc/histogram.py,sha256=0GVbDdsjd91KQ1sa2B7NtZ4KGo0XpRIJapgIrzAwQUo,5777
 ararpy/calc/isochron.py,sha256=ej9G2e68k6yszonWHsLcEubh3TA7eh1upTJP_X0ttAA,5726
 ararpy/calc/jvalue.py,sha256=OL5zPYU8Pac-wOxUWPCgu3onh2n01xDnhpi2mlUsjJM,1146
 ararpy/calc/plot.py,sha256=sUqjKBdAEjFarUoSCLqf8cbUM0rEAdZhmtyXB2K7LkA,2139
-ararpy/calc/raw_funcs.py,sha256=UPwXlYBwE1ugYRD9rsOs8JqJtm14FGcpWmUpUYJ4Roc,2744
-ararpy/calc/regression.py,sha256=mHUKobKx-Q9c7E49vPoQA2tA-MwO9BWvCp3VfnuUhUA,39776
+ararpy/calc/raw_funcs.py,sha256=GJ0VW0sc2qPIVp5jSDmPP1ClOoYRa_cc35ye7QDYOiI,2744
+ararpy/calc/regression.py,sha256=lWMoZkovtj5OEYM8eT0FcMsGrDIkKm9rsG45ru3IVuk,39798
 ararpy/calc/spectra.py,sha256=_Q23eP9necHlaCoHf3_UfW1N3JmVZj5rcWFro8GS-CA,1995
 ararpy/examples/022_VU124-M11a.ahd,sha256=3m0Gd-ZObou3KsnRNFMf77QwzT1Uz3nu3vA33Sqeyng,5414
 ararpy/examples/20WHA0103.age,sha256=cT-a4d7Wt77aotx6v0G47vulY_TZIcZUcaVHB3pqTPM,380416
@@ -33,34 +40,34 @@ ararpy/examples/WHA.pdf,sha256=iopbptHkWPmYdgihEVDDfv2nm2XE-Q-e7fFnkR44Xh0,17869
 ararpy/examples/raw_example.xls,sha256=ftcSiXRx_7nYnbqJVma1Yl3Yr_iuceAWlEjhJwlAvFM,1929895
 ararpy/examples/sample-default.smp,sha256=YNkoQGgPrsL_fXS7ZHxfRtLQWekCDqT9czS6vBScImk,432
 ararpy/files/__init__.py,sha256=l5B5ZQ01WdtvjjN0aMkyAFNgpwANdM_1I0tQbqnRuEY,69
-ararpy/files/arr_file.py,sha256=KqksGlEA6nmMQofTgi7v45flscQZVtefxaNCKrV3Am4,837
-ararpy/files/basic.py,sha256=nc7Hgo_qLSkdmtKzZmd5SQ8Jy0dhW46ly4gh-oisUDs,2095
+ararpy/files/arr_file.py,sha256=pD5MxkAydL7cNq2wmKFUaOU4jHhc3MzTYrwbxZ3f46w,881
+ararpy/files/basic.py,sha256=mGYP7QJBtyasVAYcwT0a9k6tPlcStxASddgzbaxYKkE,2105
 ararpy/files/calc_file.py,sha256=wbt-cQhPnFJ32QyofXvjCPPehmWSj4CHnidkrP7dFgk,28694
 ararpy/files/new_file.py,sha256=efblARIBROVLWS2w3-98BxLX5VZ8grRpiTkJFtf_rAk,214
-ararpy/files/raw_file.py,sha256=AUvx5Uh3aTQvGy7mXQ7771CeqFZ8u-KgdJvVOD-pU8k,21557
+ararpy/files/raw_file.py,sha256=3vGinbUyTWyQ57jMFIuckrPkN0TrNe1hqKCOAWaj70A,21854
 ararpy/files/xls.py,sha256=DVcZ_yRnc19p-m4leGGjt-YPDpSa2udYKmGyrM0qub0,640
 ararpy/smp/EXPORT_TO_PDF_DATA_PROPERTIES.py,sha256=baDM437tu6hsPv0uYfod0TREXlPd6kvMBFT1S9ZZlkk,3024
 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/diffusion_funcs.py,sha256=4-PMMIZWzjk2HOYYWNgSp4GmApygp1MmOxJ2g3xrqWc,175049
-ararpy/smp/export.py,sha256=eBUGx9eUHQ7EoibT-PC1HK7Zw_V1LUfuKJv56_XccUQ,117284
+ararpy/smp/corr.py,sha256=U5K1Vld55IHea_fZ7EEY_8dkvjp0f6OhpdSxf7b9WGY,26551
+ararpy/smp/diffusion_funcs.py,sha256=q0kl-AYx7TYeWc1kruKLOl4U4JosIuf1uNmkps11eUs,186694
+ararpy/smp/export.py,sha256=mWnnNg7DYIxcxyqeGXAWUS7faJmO7UHwnMVPX33_aLg,120638
 ararpy/smp/info.py,sha256=iKUELm-BuUduDlJKC1d8tKKNHbwwbNmhUg2pi6bcBvA,489
-ararpy/smp/initial.py,sha256=GFLEYxes-_PT_qgZj0Dagy_blg9JmzjO7uh3vQHbS78,17891
+ararpy/smp/initial.py,sha256=QGk7vh7JyVqalwnpd9VudQoX2Z9tyWzfIIw_cL5Sok0,18031
 ararpy/smp/json.py,sha256=BTZCjVN0aj9epc700nwkYEYMKN2lHBYo-pLmtnz5oHY,2300
-ararpy/smp/plots.py,sha256=rF0vrFu9dMt2Eu1EHiDfDRC9232M6dH0Unc_3qNDxLY,33579
+ararpy/smp/plots.py,sha256=S4TjYbR9BVxMh4pTSTYvhS-rdCz5zXg2wxdFgQlXT28,33582
 ararpy/smp/raw.py,sha256=51n-rrbW2FqeZHQyevuG7iObPLGvIBzTe414QDVM1FE,6523
-ararpy/smp/sample.py,sha256=slKiGUobEG7ZfJW6byBgc9jlWN1-zLg27iEdm-No5dw,58228
-ararpy/smp/style.py,sha256=wCygwtpCflhzwmI7u08X-feYGPytOyfR98YcgJx813c,7678
-ararpy/smp/table.py,sha256=9bNAOqAIOc0nSC3LNeqjJKUYSJSM28Ji3o9VimwMU8A,6645
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+ararpy/smp/table.py,sha256=Vq3GK9aslEuBhmvlQoUHjcs71Q6raSFYqd5veB1L9mk,6887
 ararpy/thermo/__init__.py,sha256=6VBuqTRFl403PVqOuMkVrut0nKaQsAosBmfW91X1dMg,263
 ararpy/thermo/arrhenius.py,sha256=Ass1ichHfqIAtpv8eLlgrUc1UOb3Urh1qzr1E3gLB4U,233
-ararpy/thermo/atomic_level_random_walk.py,sha256=Q97zfe2h2RaxADkoBAqd0uEiP16BFOajrTmXHMkL2EQ,25502
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-ararpy-0.1.30.dist-info/RECORD,,
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