分子動(dòng)力學(xué)模擬中的控制器（Controller）可用于修改模擬過程中的原子坐標(biāo)和原子速度等參量，實(shí)現(xiàn)對(duì)系統(tǒng)特定參量的控制。例如，控溫器可以用于實(shí)現(xiàn)NVT系綜，控壓器可用于實(shí)現(xiàn)NPT系綜。在MindSponge分子動(dòng)力學(xué)模擬框架下，控溫和控壓可以基于控制器Controller來實(shí)現(xiàn)。更多關(guān)于MindSponge分子動(dòng)力學(xué)模擬框架的信息，如安裝和基本使用等，可閱讀MindSponge專欄里的文章。

自定義Controller

Controller位于control路徑下，除了已經(jīng)定義好的一些控溫控壓算法之外，用戶還可以直接繼承Controller來實(shí)現(xiàn)自己需要的系統(tǒng)控制算法。例如，我們可以定義一個(gè)縮放原子速度的控制器：

class MyController(Controller): def construct(self, coordinate: Tensor, velocity: Tensor, **kwargs): return super().construct(coordinate, velocity/2, **kwargs)

它的功能是保持原子當(dāng)前位置不變，但是速度減半。

完整的MindSponge用例如下所示：

from mindspore import context, Tensor context.set_context(mode=context.GRAPH_MODE, device_target='GPU', device_id=0) from sponge import set_global_units, Sponge, Molecule, WithEnergyCell, UpdaterMD, ForceField from sponge.function import VelocityGenerator from sponge.callback import RunInfo from sponge.control import Controller # 自定義控制器 class MyController(Controller): def construct(self, coordinate: Tensor, velocity: Tensor, **kwargs): return super().construct(coordinate, velocity/2, **kwargs) # 設(shè)置全局分子動(dòng)力學(xué)模擬單位 set_global_units('nm', 'kj/mol') # 根據(jù)內(nèi)置模板生成水分子系統(tǒng) system = Molecule(template='water.spce.yaml') # 將分子沿X軸方向復(fù)制一份，現(xiàn)在體系有2個(gè)水分子 system.reduplicate([0.3, 0, 0]) # 基于前面的分子系統(tǒng)，再?gòu)?fù)制一份，然后合并到system里面，此時(shí)一共是4個(gè)水分子 new_sys = system.copy([0, 0, -0.3]) system.append(new_sys) # 選擇SPCE力場(chǎng) potential = ForceField(system, parameters='SPCE') # 類似于深度學(xué)習(xí)中的WithLossCell，綁定了分子系統(tǒng)和力場(chǎng)的信息 withenergy = WithEnergyCell(system, potential) # 配置MD參數(shù) temp = 300 vgen = VelocityGenerator(temp) velocity = vgen(system.shape, system.atom_mass) # 構(gòu)建迭代器，并且傳入我們自定義的控制器 updater = UpdaterMD( system=system, time_step=1e-3, velocity=velocity, integrator='velocity_verlet', temperature=300, controller=MyController(system), ) # 綁定系統(tǒng)、力場(chǎng)和迭代器三者的內(nèi)容 mini = Sponge(withenergy, optimizer=updater) # 使用回調(diào)函數(shù)，每一步都會(huì)打印輸出能量、溫度等信息 run_info = RunInfo(1) mini.run(5, callbacks=[run_info])

因?yàn)槊看慰刂破鞅徽{(diào)用都會(huì)使得速度減半，而且按照?qǐng)?zhí)行的順序，控制器在常規(guī)的控溫之后，因此運(yùn)行過程中體系的溫度無(wú)法達(dá)到我們預(yù)期的300K。

如果去掉這個(gè)降低速度的控制器，那么體系的溫度和動(dòng)能一下子就上去了，并且在穩(wěn)定之后，溫度會(huì)逐漸收斂在300K附近。

總結(jié)概要

本文介紹了在MindSponge分子動(dòng)力學(xué)模擬框架先實(shí)現(xiàn)自定義Controller控制器的方法，通過調(diào)控體系中的原子坐標(biāo)和原子速度等，來控制系綜的參量。MindSponge分子模擬框架基于MindSpore深度學(xué)習(xí)框架開發(fā)而成，對(duì)于開發(fā)者尤其是深度學(xué)習(xí)開發(fā)者來說，非常的友好。

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