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* utils/analyze: PEP8 fixAaron LI2019-02-251-1/+1
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* utils/analyze: Extend loglinfit() to accept x/y limitsAaron LI2019-02-241-5/+27
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* utils/analyze: Add parameter 'coef0' to loglinfit()Aaron LI2019-02-241-3/+6
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* utils/analyze: Improve logfit() to output uncertaintiesAaron LI2019-02-221-8/+25
| | | | | | | Use ``scipy.optimize.curve_fit()`` to do the underlying fitting, which can give the uncertainties of the fitted parameters. Rename logfit() to loglinfit().
* clusters/halo: Support merger-disabled calculationAaron LI2019-02-221-16/+20
| | | | | | | | | | Change the 'is_end' parameter in tau_acceleration() method to 'has_merger', which describes whether or not the merger-induced turbulence is enabled. Update the fp_diffusion() method to properly calculate the acceleration timescale (tau) in all supported situations (e.g., with merger disabled to derive the fiducial results).
* clusters/halo: Rename '_acceleration_disabled' to '_merger_disabled'Aaron LI2019-02-211-11/+12
| | | | | | | | Since there may be base turbulence that can (gentlely) accelerate the electrons, the original name '_acceleration_disabled' is no longer accurate. Change it to '_merger_disabled', which better describes that we disable the *merger-induced* turbulence that can greatly accelerate the electrons.
* clusters/halo: Clean up _is_turb_active()Aaron LI2019-02-211-7/+4
| | | | | | | Do not check 'self._acceleration_disabled'. This will be reworked in a moment. Clean up the code.
* utils/unit: Minor cleanupsAaron LI2019-02-211-6/+10
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* clusters/halo: Minor tweaksAaron LI2019-02-211-4/+5
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* clusters/halo: Update fp_diffusion() against base turbulenceAaron LI2019-02-211-2/+8
| | | | | | When the (merger-induced) turbulence is not active, invoke the tau_acceleration() with 'is_end=True' to calculate the acceleration timescale w.r.t. the base turbulence.
* clusters/halo: Extend tau_acceleration() against base turbulenceAaron LI2019-02-211-10/+32
| | | | | | Add new parameter 'is_end' to this method. If it is True, then calculate the acceleration timescale using velocity_turb_base(), i.e., the situation without active merger-induced turbulence.
* clusters/halo: Update velocity_turb() against base turbulenceAaron LI2019-02-211-13/+16
| | | | | Take into account the base turbulence by using the newly added velocity_turb_base() method.
* clusters/halo: Remove unused mach_turb() methodAaron LI2019-02-211-10/+0
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* clusters/halo: Add velocity_turb_base() methodAaron LI2019-02-212-0/+46
| | | | | | | | | | This method calculates the velocity dispersion of the base turbulence, i.e., the turbulence existing in a relaxed system without the merger injection. Add new configuration option 'extragalactic/halos/x_turb' to parameterize the energy fraction of the base turbulence w.r.t. the ICM thernal energy.
* clusters/halo: Implement _merger_end_time() methodAaron LI2019-02-211-0/+18
| | | | | Determine the ending time of the most recent merger happened before the given time.
* clusters/halo: Several minor improvementsAaron LI2019-02-211-4/+5
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* clusters/halo: Reorder '_is_turb_active()' a bitAaron LI2019-02-211-11/+11
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* clusters/halo: Reorder the '_energy_loss()' methodAaron LI2019-02-211-33/+21
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* clusters/halo: Clean up fp_advection()Aaron LI2019-02-211-7/+2
| | | | | The check of _is_turb_active() is not needed, which is actually a bit wrong, since the calculation of 'electron_spec_init' was updated.
* clusters/halo: Extends _validate_time() with 'include_end' parameterAaron LI2019-02-211-6/+8
| | | | | | | Check the time against the merge end time only if 'include_end' is True (the default). Specify 'include_end=False' in duration_turb() method.
* clusters/halo: Apply @property and @lru_cache() to _time_adjust()Aaron LI2019-02-211-1/+3
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* clusters/halo: Update _validate_t_merger() to also check end timeAaron LI2019-02-211-11/+12
| | | | | Rename '_validate_t_merger()' to '_validate_time()' and update this method to also check the end time of a merger.
* clusters/halo: Add 't_merger_end' propertyAaron LI2019-02-211-9/+30
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* configs/spec: Adjust some min/max values for simplicityAaron LI2019-02-211-5/+5
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* clusters/halo: Further extend the halo radius calculationAaron LI2019-02-182-14/+15
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* clusters/halo: Improve the halo radius calculationAaron LI2019-02-161-2/+23
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* clusters/halo: Clean up the magnetic field calculation a bitAaron LI2019-02-161-3/+4
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* clusters/main: Adjust log level for _simulate_halo1()Aaron LI2019-02-161-2/+2
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* clusters/main: Minor cleanupsAaron LI2019-02-011-2/+8
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* clusters/helper: Some cleanupsAaron LI2019-01-311-32/+13
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* clusters: Use radius_cluster() accordinglyAaron LI2019-01-313-17/+14
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* clusters/helper: Remove obsolete time_crossing()Aaron LI2019-01-311-31/+0
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* clusters/helper: Add radius_cluster()Aaron LI2019-01-311-0/+19
| | | | Ignore the cosmic evolution, keeping the radio halo modeling simple.
* clusters/main: Skip drawing ingenuine halosAaron LI2019-01-301-3/+3
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* clusters/main: Also calculate spectral index and acceleration factorAaron LI2019-01-301-7/+22
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* clusters/main: Add 'genuine' property for halosAaron LI2019-01-302-1/+13
| | | | Configuration option 'genuine_threshold' is added together.
* clusters: Minor cleanups (rename 'comp' to 'sec')Aaron LI2019-01-303-47/+49
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* clusters/main: Improve keys handling in _save_halos_data()Aaron LI2019-01-301-3/+2
| | | | This also fixes the issue when try to remove a non-existent key.
* utils/analyze: Add countdist() functionAaron LI2019-01-301-8/+16
| | | | Modified from the original countdist_integrated().
* clusters/psformalism: Count for dark matter fraction for M_minAaron LI2019-01-292-6/+8
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* clusters/halo: Add options bolo_freq_{min,max,num}Aaron LI2019-01-293-3/+18
| | | | Update the default bolometric frequency band to: 10 MHz -- 100 GHz.
* clusters/helper: Get rid of CONFIGSAaron LI2019-01-291-37/+7
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* clusters/formation: Add show() methodAaron LI2019-01-291-1/+9
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* clusters/formation: Move history() to mergertree.get_history()Aaron LI2019-01-292-30/+46
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* clusters/main: Do not require "age" in _simulate_mergers()Aaron LI2019-01-291-4/+3
| | | | Thus _simulate_mergers() can be called without _process_catalog().
* utils/healpix: Minor cleanupsAaron LI2019-01-291-22/+36
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* Use UTC time instead of local timeAaron LI2019-01-293-22/+17
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* clusters/formation: Implement history() methodAaron LI2019-01-291-16/+36
| | | | | | | Compared to the original mergers() method, this method extracts all formation history (i.e., both mergers and accretions). The mergers() method is now simply wraps on the history() method.
* clusters/mergertree: Tweak format of show_mtree() a bitAaron LI2019-01-281-3/+3
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* clusters/megertree: Minor cleanupsAaron LI2019-01-281-7/+9
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