diff --git a/MindSPONGE/docs/1631067726523.png b/MindSPONGE/docs/1631067726523.png new file mode 100644 index 0000000000000000000000000000000000000000..bae1549448c9084de844023a3f878b389674fc2a Binary files /dev/null and b/MindSPONGE/docs/1631067726523.png differ diff --git a/MindSPONGE/docs/1631069737509.png b/MindSPONGE/docs/1631069737509.png new file mode 100644 index 0000000000000000000000000000000000000000..e4070222bc3715c362c4c2341676e0c18f1c8786 Binary files /dev/null and b/MindSPONGE/docs/1631069737509.png differ diff --git a/MindSPONGE/docs/1631069990374.png b/MindSPONGE/docs/1631069990374.png new file mode 100644 index 0000000000000000000000000000000000000000..11ad86a8dbbd853149d21f9f08e37b4b8c8e6793 Binary files /dev/null and b/MindSPONGE/docs/1631069990374.png differ diff --git a/MindSPONGE/mindsponge/md/control/langevin_liujian_md.py b/MindSPONGE/mindsponge/md/control/langevin_liujian_md.py index dfe6d7821d4815604c183799acfbe39e50d82bc7..9398b4d035235b7356b78a92d50fbb196d3693ff 100644 --- a/MindSPONGE/mindsponge/md/control/langevin_liujian_md.py +++ b/MindSPONGE/mindsponge/md/control/langevin_liujian_md.py @@ -62,7 +62,7 @@ class LangevinLiujian: for i in range(self.atom_numbers): self.h_sqrt_mass[i] = self.sqrt_gamma * math.sqrt(1. / self.h_mass[i]) if self.h_mass[i] != 0 else 0 - self.max_velocity = 0 + self.max_velocity = 0.0 if "velocity_max" in controller.command_set: self.max_velocity = float(controller.command_set["velocity_max"]) if "langevin_liu_velocity_max" in controller.command_set: diff --git a/MindSPONGE/protein_msa/README_CN.md b/MindSPONGE/protein_msa/README_CN.md index fd7d14576a562b43938bc0f2ea38ef0b5a2e3932..6a87c1727aa9bcc94b4bd2b9f30144f48e41368e 100644 --- a/MindSPONGE/protein_msa/README_CN.md +++ b/MindSPONGE/protein_msa/README_CN.md @@ -67,6 +67,87 @@ Browser+的不同账号,与注册的云服务账号无关,也无需一致。 ![1630459406400](../docs/20210903-150630.gif) +#### 使用obsutil命令行工具进行数据集的下载 + +##### 安装命令行工具 + +安装详细官方指导,请参考华为云文档资料:[https://support.huaweicloud.com/utiltg-obs/obs_11_0003.html](https://support.huaweicloud.com/utiltg-obs/obs_11_0003.html) 。 此处我们仅提供Ubuntu 18.04的操作系统上安装的流水账步骤: + +打开你的Terminal,cd 到你期望的安装目录,依次执行如下四个命令: + +```shell +wget https://obs-community.obs.cn-north-1.myhuaweicloud.com/obsutil/current/obsutil_linux_amd64.tar.gz + +tar -xzvf obsutil_linux_amd64.tar.gz + +cd obsutil_linux_amd64_* + +chmod 755 obsutil +``` + +执行成功后,如下图所示: + +![1630473600777](../docs/20210903-150615.png) + +##### 初始化配置 + +执行如下命令, 其中ak, sk是你在之前步骤中已经准备好的账号鉴权信息。 endpoint固定为:https://obs.cn-north-4.myhuaweicloud.com + +```shell +./obsutil config -i=ak -k=sk -e=endpoint +``` + +执行成功后,如下图所示: + +![1630473997617](../docs/20210903-150619.png) + +##### 列表文件 + +详细官方指导,请参考华为云文档资料:[https://support.huaweicloud.com/utiltg-obs/obs_11_0014.html](https://support.huaweicloud.com/utiltg-obs/obs_11_0014.html) + +此处我们仅提供Ubuntu 18.04的操作系统上的流水账步骤: + +打开你的Terminal,cd 到你obsutil的安装目录,通过以下命令列表数据集内的文件/文件夹,执行效果如下图所示 + +```shell +./obsutil ls obs://cnnorth4-modelhub-datasets-obsfs-d1opw/MSA_Uniref50 -d +``` + +![1631067726523](../docs/1631067726523.png) + +##### 递归下载目录 + +详细官方指导,请参考华为云文档资料:[https://support.huaweicloud.com/utiltg-obs/obs_11_0018.html](https://support.huaweicloud.com/utiltg-obs/obs_11_0018.html) + +此处我们仅提供Ubuntu 18.04的操作系统上流水账步骤: + +打开你的Terminal,cd 到你obsutil的安装目录,通过以下命令递归下载目录,执行效果如下图所示 + +```shell +./obsutil cp obs://cnnorth4-modelhub-datasets-obsfs-d1opw/MSA_Uniref50/Example_100G /root/mas_demo_detasets -r -f +``` + +![1631069737509](../docs/1631069737509.png) + +##### 增量同步递归下载目录 + +使用场景: + +- 当上述递归下载目录出现有些文件下载失败的场景,可以使用这个命令,自动检测缺失的文件,并下载 +- 下载数据的电脑因为意外重启了,需要继续断点续传 + +详细官方指导,请参考华为云文档资料:[https://support.huaweicloud.com/utiltg-obs/obs_11_0043.html](https://support.huaweicloud.com/utiltg-obs/obs_11_0043.html) + +此处我们仅提供Ubuntu 18.04的操作系统上流水账步骤: + +打开你的Terminal,cd 到你obsutil的安装目录,通过以下命令增量同步递归下载目录,执行效果如下图所示 + +```shell +./obsutil sync obs://cnnorth4-modelhub-datasets-obsfs-d1opw/MSA_Uniref50/Example_100G /root/mas_demo_detasets +``` + +![1631069990374](../docs/1631069990374.png) + ## 维护、更新与社区贡献方式 ### 如何贡献数据集